U.S. patent number 9,387,476 [Application Number 14/729,809] was granted by the patent office on 2016-07-12 for flow cells for biological or chemical analysis.
This patent grant is currently assigned to Illumina, Inc.. The grantee listed for this patent is ILLUMINA, INC.. Invention is credited to Majid Aghababazadeh, Helmy A. Eltoukhy, Behnam Javanmardi, Tarun Khurana, Poorya Sabounchi.
United States Patent |
9,387,476 |
Eltoukhy , et al. |
July 12, 2016 |
Flow cells for biological or chemical analysis
Abstract
A flow cell including inlet and outlet ports in fluid
communication with each other through a flow channel that extends
therebetween. The flow channel includes a diffuser region and a
field region that is located downstream from the diffuser region.
The field region of the flow channel directs fluid along reaction
sites where desired reactions occur. The fluid flows through the
diffuser region in a first flow direction and through the field
region in a second flow direction. The first and second flow
directions being substantially perpendicular.
Inventors: |
Eltoukhy; Helmy A. (Atherton,
CA), Khurana; Tarun (Freemont, CA), Javanmardi;
Behnam (San Jose, CA), Sabounchi; Poorya (Pleasant Hill,
CA), Aghababazadeh; Majid (Cupertino, CA) |
Applicant: |
Name |
City |
State |
Country |
Type |
ILLUMINA, INC. |
San Diego |
CA |
US |
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Assignee: |
Illumina, Inc. (San Diego,
CA)
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Family
ID: |
54141181 |
Appl.
No.: |
14/729,809 |
Filed: |
June 3, 2015 |
Prior Publication Data
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Document
Identifier |
Publication Date |
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US 20150266022 A1 |
Sep 24, 2015 |
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Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
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13882088 |
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9096899 |
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PCT/US2011/057111 |
Oct 20, 2011 |
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61407350 |
Oct 27, 2010 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
B01L
3/502715 (20130101); B01L 7/52 (20130101); C12Q
1/6869 (20130101); C12Q 1/6874 (20130101); B01L
3/5085 (20130101); B01L 2200/025 (20130101); B01L
2300/161 (20130101); B01L 2400/0457 (20130101); B01L
2300/0819 (20130101); B01L 2300/022 (20130101); B01L
2200/04 (20130101); B01L 2300/0627 (20130101); B01L
2300/0654 (20130101); B01L 2200/10 (20130101); B01L
2300/165 (20130101); B01L 2400/0487 (20130101); B01L
2300/048 (20130101); B01L 2300/023 (20130101); B01L
2300/0877 (20130101); B01L 2300/0636 (20130101); B01L
2400/0622 (20130101); B01L 2200/082 (20130101); B01L
2300/0645 (20130101); B01L 2200/16 (20130101) |
Current International
Class: |
G01N
15/06 (20060101); G01N 33/00 (20060101); G01N
33/48 (20060101); A61J 1/06 (20060101); B01L
3/00 (20060101); G01N 21/00 (20060101); C12Q
1/68 (20060101) |
Field of
Search: |
;422/50,68.1,81,502,503,504,509,554 ;436/43,63,174,180,177,178 |
References Cited
[Referenced By]
U.S. Patent Documents
Foreign Patent Documents
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1 542 010 |
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Jun 2005 |
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EP |
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1 669 754 |
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Jun 2006 |
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EP |
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1 762 300 |
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Mar 2007 |
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EP |
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02352035 |
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Jan 2010 |
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EP |
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WO 03/087410 |
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Oct 2003 |
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WO |
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WO 2006/136990 |
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Dec 2006 |
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WO |
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WO 2009/111696 |
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Sep 2009 |
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WO |
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WO 2010/010904 |
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Jan 2010 |
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WO |
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Other References
International Search Report and Written Opinion for International
Application PCT/US2011/057111, mailing date Mar. 26, 2012. cited by
applicant.
|
Primary Examiner: Sines; Brian J
Attorney, Agent or Firm: The Small Patent Law Group, LLC
Small; Dean Gross; Jason
Government Interests
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with Government support under NIH Grant
Number HG003571 awarded by the PHS. The Government has certain
rights in the invention.
Parent Case Text
CROSS REFERENCE TO RELATED APPLICATION
The present application is a continuation of U.S. application Ser.
No. 13/882,088 ("the '088 application"), filed Apr. 26, 2013, which
is a National Stage of International Application No.
PCT/US2011/057111, filed Oct. 20, 2011, which claims the benefit of
U.S. Provisional Application Ser. No. 61/407,350 ("the '350
application"), filed Oct. 27, 2010. Each of the '088 application
and the '350 application is incorporated herein by reference in its
entirety.
Claims
What is claimed is:
1. A flow cell comprising inlet and outlet ports in fluid
communication with each other through a flow channel that extends
therebetween, the flow channel including a diffuser region and a
field region that is located downstream from the diffuser region,
the flow channel also including a collector region that is located
downstream from the field region and configured to receive fluid
from the field region, the diffuser region being shaped to increase
a cross-sectional area of the flow channel as the diffuser region
extends downstream in a first fluid flow direction, the field
region of the flow channel directing fluid along reaction sites
where desired reactions occur, wherein the fluid flows through the
field region in a second flow direction, the first and second flow
directions being perpendicular, wherein the fluid is configured to
flow through the collector region in a third flow direction that is
different than the second flow direction, the collector region
being shaped to reduce a cross-sectional area of the flow channel
as the collector region extends downstream in the third flow
direction.
2. The flow cell in accordance with claim 1 wherein the first flow
direction is configured to extend along a gravitational force
direction when in operation.
3. The flow cell in accordance with claim 1 wherein a flow
cross-section of the field region is defined by dimensions that are
uniform throughout the field region.
4. A flow cell comprising inlet and outlet ports in fluid
communication with each other through a flow channel that extends
therebetween, the flow channel including a diffuser region and a
common field region that is located downstream from the diffuser
region, the field region of the flow channel directing fluid along
reaction sites where desired reactions occur, wherein the fluid
flows through the diffuser region in a first flow direction and
through the field region in a second flow direction, the first and
second flow directions being perpendicular; wherein the diffuser
region comprises a plurality of inlet channels that provide fluid
to the field region, the inlet channels being spaced apart from
each other along a dimension of the field region that extends
perpendicular to the second fluid direction.
5. The flow cell in accordance with claim 1 wherein the collector
region has a similar shape as the diffuser region.
6. The flow cell in accordance with claim 1 further comprising an
engagement area along an exterior surface that is configured to
interface with a thermal element, the engagement area extending
along the field region of the flow channel.
7. The flow cell in accordance with claim 1 wherein the diffuser
region is configured to distribute a uniform flow of fluid through
the field region.
8. The flow cell in accordance with claim 1, wherein the flow cell
includes a flow cover having the inlet and outlet ports and a
substrate layer configured to have the reaction sites, the field
region being disposed between the flow cover and the substrate
layer.
9. The flow cell in accordance with claim 8, wherein the flow cover
and the substrate layer are discrete elements that are secured to
each other, the flow cover having a mounting side, the mounting
side and the substrate layer forming the field region therebetween
when the flow cover is coupled to the substrate layer.
10. The flow cell in accordance with claim 9, wherein the flow
cover has an open-sided recess along the mounting side, the
diffuser region and the collector region opening into the
open-sided recess, the open-sided recess forming the field region
when the flow cover is coupled to the substrate layer.
11. The flow cell in accordance with claim 9, wherein the substrate
layer includes a plurality of reaction chambers that open to and
are in fluid communication with the field region, the reaction
chambers being defined by shared walls.
12. The flow cell in accordance with claim 11, wherein the
substrate layer includes thru-holes that extend entirely through
the substrate layer and form the reaction chambers, the substrate
layer configured to be mounted to an intermediate layer or activity
detector to enclose the reaction chambers.
13. The flow cell in accordance with claim 4, wherein the flow cell
includes a flow cover having the inlet and outlet ports and a
substrate layer configured to have the reaction sites, the field
region being disposed between the flow cover and the substrate
layer.
14. The flow cell in accordance with claim 13, wherein the flow
cover and the substrate layer are discrete elements that are
secured to each other, the flow cover having a mounting side, the
mounting side and the substrate layer forming the field region
therebetween when the flow cover is coupled to the substrate
layer.
15. The flow cell in accordance with claim 14, wherein the flow
cover has an open-sided recess along the mounting side, the inlet
channels opening to the open-sided recess, the open-sided recess
forming the field region when the flow cover is coupled to the
substrate layer.
16. The flow cell in accordance with claim 14, wherein the
substrate layer includes a plurality of reaction chambers that open
to and are in fluid communication with the field region, the
reaction chambers being defined by shared walls.
17. The flow cell in accordance with claim 16, wherein the
substrate layer includes thru-holes that extend entirely through
the substrate layer and form the reaction chambers, the substrate
layer configured to be mounted to an intermediate layer or activity
detector to enclose the reaction chambers.
18. The flow cell in accordance with claim 4, wherein the flow cell
includes a platform that has the inlet port and the diffuser
region, the platform having a cavity that opens to an exterior of
the platform, the cavity being partially filled with a plug to
separate the cavity from the exterior and form the diffuser
region.
19. The flow cell in accordance with claim 18, wherein the platform
is a first platform and the flow cell includes a second platform
that includes a collector region, the flow cell having an
engagement area along an exterior surface that is configured to
interface with a thermal element, the engagement area extending
along the field region of the flow channel between the first and
second platforms.
Description
BACKGROUND OF THE INVENTION
Embodiments of the present invention relate generally to biological
or chemical analysis and more particularly, to systems and methods
using microfluidic and detection devices for biological or chemical
analysis.
Various protocols in biological or chemical research involve
performing a large number of controlled reactions on local support
surfaces or within predefined reaction chambers. The desired
reactions may then be observed or detected, and subsequent analysis
may help identify or reveal properties of chemicals involved in the
reaction. For example, in some multiplex assays, an unknown analyte
having an identifiable label (e.g., fluorescent label) may be
exposed to thousands of known probes under controlled conditions.
Each known probe may be deposited into a corresponding well of a
microplate. Observing any chemical reactions that occur between the
known probes and the unknown analyte within the wells may help
identify or reveal properties of the analyte. Other examples of
such protocols include known DNA sequencing processes, such as
sequencing-by-synthesis or cyclic-array sequencing. In cyclic-array
sequencing, a dense array of DNA features (e.g., template nucleic
acids) are sequenced through iterative cycles of enzymatic
manipulation. After each cycle, an image may be captured and
subsequently analyzed with other images to determine a sequence of
the DNA features.
As a more specific example, one known DNA sequencing system uses a
pyrosequencing process and includes a chip having a fused
fiber-optic faceplate with millions of wells. A single capture bead
having clonally amplified sstDNA from a genome of interest is
deposited into each well. After the capture beads are deposited
into the wells, nucleotides are sequentially added to the wells by
flowing a solution containing a specific nucleotide along the
faceplate. The environment within the wells is such that if a
nucleotide flowing through a particular well complements the DNA
strand on the corresponding capture bead, the nucleotide is added
to the DNA strand. Incorporation of the nucleotide into the DNA
strand initiates a process that ultimately generates a
chemiluminescent light signal. The system includes a CCD camera
that is positioned directly adjacent to the faceplate and is
configured to detect the light signals from the wells. Subsequent
analysis of the images taken throughout the pyrosequencing process
can determine a sequence of the genome of interest.
However, the above pyrosequencing system, in addition to other
systems, may have certain limitations. For example, the fiber-optic
faceplate is acid-etched to make millions of small wells. Although
the wells may be approximately spaced apart from each other, it is
difficult to know a precise location of a well in relation to other
adjacent wells. When the CCD camera is positioned directly adjacent
to the faceplate, the wells are not evenly distributed along the
pixels of the CCD camera and, as such, the wells are not aligned in
a known manner with the pixels. Inter-well crosstalk between the
adjacent wells makes distinguishing true light signals from the
well of interest from other unwanted light signals difficult in the
subsequent analysis. As a result, data recorded during the
sequencing cycles must be carefully analyzed. Furthermore, the
above system uses a high-resolution camera (16 Megapixels) to
determine true signals from unwanted crosstalk. However, the
high-resolution camera generates large amounts of data that must be
analyzed that, in turn, may slow down the process. The
high-resolution camera can also be expensive.
Furthermore, the above pyrosequencing system may use a number of
enzymatic strategies to reduce crosstalk. For example, the system
may use apyrase to degrade unincorporated nucleotide species and
ATP, exonuclease to degrade linear nucleic acid molecules,
pyrophosphatase (also referred to as PPi-ase) to degrades PPi,
and/or enzymes to inhibit activity of other enzymes. However, these
enzymatic strategies may increase the total costs of sequencing and
may also negatively affect the system's ability to discern the true
light signals for a certain well.
Moreover, sequencing systems and other bioassay systems must
fluidicly deliver reagents and enzymes to the wells or other
reaction sites and remove the unused reagents and enzymes. Some
challenges that arise in delivering/removing the reagents and
enzymes include bubble formation within a fluidic system. Bubbles
disrupt the flow of the fluids through the faceplate as well as
negatively affect the imaging of a reaction sites. Furthermore, if
a system does not have uniform flow through the faceplate, then
some wells may not be properly washed or may receive the reagents
at different times or in different concentrations with respect to
other wells in the chip. This may lead to misleading or incorrect
data.
Bioassay systems are also typically configured to perform only one
assay protocol or very similar protocols. For example, the CCD
camera in the pyrosequencing system described above may have unique
features and be configured to detect light signals emitted from the
wells of the faceplate. However, the features and predetermined
configuration of the CCD camera may not be suitable for other types
of sequencing protocols or other assay protocols. As such, the
system may be limited to only those protocols that require the CCD
camera to be predisposed in a similar way.
In addition to the above challenges and limitations, there is a
general need for more user-friendly bioassay systems that reduce
costs relative to other known systems and also increase control and
efficiency of the reactions intended to be observed.
BRIEF DESCRIPTION OF THE INVENTION
In accordance with one embodiment, a biosensor cartridge configured
to engage a bioassay system is provided. The biosensor cartridge
includes a flow cell having inlet and outlet ports and a flow
channel that extends therebetween. The flow cell can include a
substrate field comprising a plurality of reaction chambers. The
reaction chambers have apertures that open onto the flow channel
such that the reaction chambers are in fluid communication with the
flow channel. The biosensor cartridge can also include an activity
detector that is coupled to the flow cell and has an array of
pixels that have a fixed positioned relative to the substrate
field. The pixels may be assigned to select reaction chambers such
that activity detected by the pixels indicates that a desired
reaction has occurred within the select reaction chamber. The
biosensor cartridge also includes an exterior side surface that has
a plurality of electrical contacts thereon that are communicatively
coupled to the pixels. The electrical contacts of the side surface
are configured to engage corresponding mating contacts of a
bioassay system.
In another embodiment, a biosensor cartridge that is configured to
removably engage a bioassay system is provided. The biosensor
cartridge includes a flow cell having inlet and outlet ports and a
flow channel that extends therebetween. The biosensor cartridge
also includes an activity detector that is coupled to the flow cell
and is configured to detect activity along the flow channel that is
indicative of desired reactions. The biosensor cartridge may also
have first and second side surfaces. The first side surface can
include the inlet and outlet ports. The second side surface can
include electrical contacts that are communicatively coupled to the
activity detector. The first and second side surfaces may face in
substantially opposite directions.
In yet another embodiment, a flow cell is provided that includes
inlet and outlet ports in fluid communication with each other
through a flow channel that extends therebetween. The flow channel
has a diffuser region and a field region that is located downstream
from the diffuser region. The field region of the flow channel
directs fluid along reaction sites where desired reactions occur.
The fluid flows through the diffuser region in a first flow
direction and through the field region in a second flow direction.
The first and second flow directions can be substantially
perpendicular to each other.
In a further embodiment, a workstation for biological or chemical
analysis is provided. The workstation includes a receptacle that is
configured to receive and establish electrical and fluidic
couplings with a microdevice and a fluidic control system for
controlling a flow of fluid through the microdevice. The fluidic
control system includes an upstream conduit for delivering the
fluid and a downstream conduit for removing the fluid. The
workstation also includes a user interface that is configured to
receive user selections or inputs and a system controller that
includes an identification module and a protocol module. The
identification module is configured to receive signals relating to
identification information of the microdevice. The protocol module
is configured to determine at least one parameter of an assay
protocol based at least in part on the identification information.
An operation of the fluidic control system is based at least in
part on the determined at least one parameter.
In another embodiment, a system receptacle that is configured to
engage a biosensor cartridge is provided. The system receptacle
includes an alignment assembly that is configured to hold the
biosensor cartridge in a predetermined orientation. The system
receptacle also includes an upstream conduit for delivering fluid
to the biosensor cartridge and a downstream conduit for removing
the fluid from the biosensor cartridge. The upstream and downstream
conduits include respective nozzles. The system receptacle also
includes an actuation device that is configured to move the nozzles
of the upstream and downstream conduits toward the biosensor
cartridge in an axial direction to establish a fluidic
connection.
In a further embodiment, a workstation for biological or chemical
analysis is provided. The workstation includes a workstation
housing and a fluidic-control system at least partially positioned
within the housing. The fluidic-control system includes an upstream
conduit for delivering fluid to a biosensor cartridge and a
downstream conduit for removing the fluid from the biosensor
cartridge. The system receptacle is configured to receive the
biosensor cartridge. The system receptacle includes an alignment
assembly that is configured to hold the biosensor cartridge in a
predetermined orientation and upstream and downstream nozzles
fluidicly coupled to the upstream and downstream conduits,
respectively. The system receptacle also includes an actuation
device that is configured to move the nozzles of the upstream and
downstream conduits toward the alignment assembly in an axial
direction to establish a fluidic connection with the biosensor
cartridge.
In yet another embodiment, a reservoir bag is provided that has top
and bottom ends and a height extending therebetween. A
gravitational force direction is configured to extend from the top
end to the bottom end when the reservoir bag is in operation. The
reservoir bag includes at least one flexible wall that defines a
variable volume for holding a fluid. The volume has a main storage
portion, a flow path portion, and a bridge portion. The main
storage portion and the flow path portion are in fluid
communication with each other through the bridge portion. The
reservoir bag also includes a bag opening that is located proximate
to the top end. The fluid flowing through the bag opening when the
fluid is removed. The reservoir bag also includes a partition that
projects from the top end toward the bottom end to a distal tip and
separates the main storage and flow path portions. The bridge
portion is located between the distal tip and the bottom end.
In one embodiment, a bioassay system is provided that is configured
to engage a microdevice for performing desired reactions and
detecting activity that is indicative of the desired reactions. The
bioassay system includes a system receptacle configured to engage
the microdevice and a fluidic-control system that is configured to
control a flow of fluid through the microdevice. The
fluidic-control system is in fluid communication with the
microdevice. The bioassay system also includes a fluid storage
system that is fluidicly coupled to the fluidic-control system. The
fluid storage system is configured to provide reagents to be used
for the desired reactions within the microdevice. The bioassay
system also includes a temperature control system and a user
interface that is configured to receive user inputs from a user of
the bioassay system. Furthermore, the bioassay system includes a
system controller that is configured to control operation of the
fluidic-control, the fluid storage, and the temperature control
systems. The system controller is also configured to receive the
user inputs from the user interface. The user inputs may relate to
an assay protocol to run when the microdevice is engaged. The
system controller may also communicate detection data to the user
interface. The user interface can display the detection data to the
user.
In another embodiment, a method of manufacturing a biosensor
cartridge is provided. The method comprises providing a base
substrate including an activity detector that has an array of
pixels and circuitry for communicating data regarding activity
detected by the pixels. The base substrate has an exterior side
surface that includes a plurality of electrical contacts thereon
that are communicatively coupled to the pixels through the
circuitry. The method also includes mounting a substrate layer over
the array of pixels. The substrate layer can include a plurality of
reaction chambers where desired reactions are conducted. The
substrate layer is mounted over the array of pixels such that the
pixels are assigned to select reaction chambers. Activity detected
by the assigned pixels indicates that a desired reaction has
occurred within the select reaction chamber.
In yet another embodiment, a method of conducting an assay protocol
using directed condensation is provided. The method includes
providing a flow cell that has a flow channel and a substrate layer
having a plurality of reaction chambers therein that are in fluid
communication with the flow channel. The flow cell includes a cover
wall that is spaced apart from the substrate layer. The cover wall
separates the flow channel and an exterior side surface. The flow
channel directs a flow of fluid between the cover wall and the
substrate layer. The method also includes interfacing a thermal
element with an engagement area of the side surface. The thermal
element is configured to transfer or absorb thermal energy of the
fluid in the flow channel through the cover wall. The method also
includes providing thermal energy to the fluid within the flow
channel during an assay protocol. The thermal energy is absorbed by
the fluid within the flow channel and transferred to the fluid
within the reaction chambers.
In another embodiment, a method of amplifying and sequencing DNA
within a flow cell is provided. The method includes providing a
flow cell that has a flow channel and a substrate layer having a
plurality of reaction chambers therein that are in fluid
communication with the flow channel. The flow cell includes a cover
wall that is spaced apart from the substrate layer and defines the
flow channel therebetween. The flow channel directs a flow of fluid
between the cover wall and the substrate layer. The reaction
chambers include DNA samples therein. The method also includes
flowing a first aqueous solution that includes at least one of
reagents and enzymes for DNA amplification through the flow
channel. The method also includes flowing a non-polar liquid
through the flow channel such that the first aqueous solution is
substantially removed from the flow channel. The reaction chambers
include the first aqueous solution therein that interfaces with the
non-polar liquid in the flow channel. The method also includes
controlling a temperature of the first aqueous solution in the
reaction chambers to perform DNA amplification and flowing a second
aqueous solution through the flow channel to remove the first
aqueous solution. Furthermore, the method includes flowing a third
aqueous solution through the flow channel that includes at least
one of reagents and enzymes for DNA sequencing.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a block diagram of a system for biological or chemical
analysis formed in accordance with one embodiment.
FIG. 2 is a block diagram of a system controller that may be used
in the system of FIG. 1.
FIG. 3 is a block diagram of a workstation for biological or
chemical analysis in accordance with one embodiment.
FIG. 4 provides perspective views of the workstation of FIG. 3.
FIG. 5 is a partially exploded perspective view of a biosensor
cartridge formed in accordance with one embodiment.
FIG. 6 shows plan views of the biosensor cartridge of FIG. 5.
FIG. 7 illustrates a cross-section of a microdevice formed in
accordance with one embodiment.
FIG. 8 illustrates a perspective view of a portion of the
microdevice shown in FIG. 7.
FIG. 9 is a plan view of a reaction chamber that may be used with
the microdevice of FIG. 7.
FIG. 10 is a schematic illustration of an exemplary activity
detector formed in accordance with various embodiments.
FIG. 11 is an image of a fiber-optic faceplate that may be used in
various embodiments.
FIG. 12 is a cross-section of the faceplate shown in FIG. 11.
FIG. 13 is a top perspective view of a flow cover that may be used
in various embodiments.
FIG. 14 is a bottom perspective view of the flow cover of FIG.
13.
FIG. 15 is a top perspective view of another flow cover that may be
used in various embodiments.
FIG. 16 is a bottom perspective view of another flow cover that may
be used in various embodiments.
FIG. 17 is a top perspective of the flow cover in FIG. 16.
FIG. 18 is a top perspective view of a flow cover formed in
accordance with another embodiment.
FIG. 19 is a top perspective view of a flow cover formed in
accordance with another embodiment.
FIG. 20 illustrates an exemplary embodiment of a planar flow cover
formed in accordance with various embodiments.
FIG. 21 is a top view of a biosensor cartridge formed in accordance
with one embodiment including the flow cover of FIG. 20.
FIG. 22 is a bottom view of the biosensor cartridge of FIG. 21.
FIG. 23 is a perspective view of a system receptacle formed in
accordance with one embodiment.
FIG. 24 is a bottom perspective view of a mounting assembly of the
system receptacle of FIG. 23.
FIG. 25 is a perspective view of an alignment assembly that may be
used with the system receptacle of FIG. 23.
FIG. 26 is a cross-section of the system receptacle in the
unengaged position.
FIG. 27 is a different cross-section of the system receptacle in
the engaged position.
FIG. 28 is a partial perspective view of a fluid storage unit
formed in accordance with one embodiment.
FIG. 29 is a top plan view of the storage unit of FIG. 28.
FIG. 30 is a side view of a fluid reservoir bag formed in
accordance with one embodiment.
FIG. 31 is a cross-section of the biosensor cartridge shown in FIG.
5.
DETAILED DESCRIPTION OF THE INVENTION
Embodiments described herein may be used in various biological or
chemical processes and systems for academic or commercial analysis.
More specifically, embodiments described herein may be used in
various processes and systems where it is desired to detect an
event, property, quality, or characteristic that is indicative of a
desired reaction. For example, embodiments described herein include
biosensor cartridges, microdevices, and their components as well as
bioassay systems that operate with the biosensor cartridges and
microdevices. In particular embodiments, the biosensor cartridges
and microdevices include a flow cell and an activity detector that
are coupled together in a substantially unitary structure.
The bioassay systems may be configured to perform a plurality of
desired reactions that may be detected individually or
collectively. The microdevices and bioassay systems may be
configured to perform numerous cycles where the plurality of
desired reactions occur in parallel. For example, the bioassay
systems may be used to sequence a dense array of DNA features
through iterative cycles of enzymatic manipulation and image
acquisition. As such, the biosensor cartridges and microdevices may
include one or more microfluidic channels that deliver reagents or
other reaction components to a reaction site. In some embodiments,
the reaction sites are reaction chambers that compartmentalize the
desired reactions therein. Furthermore, embodiments may include an
activity detector that is configured to detect activity that is
indicative of the desired reactions.
As used herein, a "desired reaction" includes a change in at least
one of a chemical, electrical, physical, and optical property or
quality of a substance that is in response to a stimulus. For
example, the desired reaction may be a chemical transformation,
chemical change, or chemical interaction. The desired reaction may
also be a change in electrical properties. For example, the desired
reaction may be a change in ion concentration within a solution.
Exemplary reactions include, but are not limited to, chemical
reactions such as reduction, oxidation, addition, elimination,
rearrangement, esterification, amidation, etherification,
cyclization, or substitution; binding interactions in which a first
chemical binds to a second chemical; dissociation reactions in
which two or more chemicals detach from each other; fluorescence;
luminescence; chemiluminescence; and biological reactions, such as
nucleic acid replication, nucleic acid amplification, nucleic acid
hybridization, nucleic acid ligation, phosphorylation, enzymatic
catalysis, receptor binding, or ligand binding. The desired
reaction can also be addition or elimination of a proton, for
example, detectable as a change in pH of a surrounding solution or
environment.
The stimulus can be at least one of physical, optical, electrical,
magnetic, and chemical. For example, the stimulus may be an
excitation light that excites fluorophores in a substance. The
stimulus may also be a change in a surrounding environment, such as
a change in concentration of certain biomolecules (e.g., enzymes or
ions) in a solution. The stimulus may also be an electrical current
applied to a solution within a predefined volume. In addition, the
stimulus may be provided by shaking, vibrating, or moving a
reaction chamber where the substance is located to create a force
(e.g., centripetal force). As used herein, the phrase "in response
to a stimulus" is intended to be interpreted broadly and include
more direct responses to a stimulus (e.g., when a fluorophore emits
energy of a specific wavelength after absorbing incident excitation
light) and more indirect responses to a stimulus in that the
stimulus initiates a chain of events that eventually results in the
response (e.g., incorporation of a base in pyrosequencing
eventually resulting in chemiluminescence). The stimulus may be
immediate (e.g., excitation light incident upon a fluorophore) or
gradual (e.g., change in temperature of the surrounding
environment).
As used herein, the phrase "activity that is indicative of a
desired reaction" and grammatical variants thereof include any
detectable event, property, quality, or characteristic that may be
used to facilitate determining whether a desired reaction has
occurred. For example, the detected activity may be a light signal
generated in fluorescence or chemiluminescence. The detected
activity may also be a change in electrical properties of a
solution within a predefined volume or along a predefined area. The
detected activity may be a change in temperature.
As used herein, a "reaction component" or "reactant" includes any
substance that may be used to obtain a desired reaction. For
example, reaction components include reagents, enzymes, samples,
other biomolecules, and buffer solutions. The reaction components
are typically delivered to a reaction site in a solution or
immobilized within a reaction site. The reaction components may
interact directly or indirectly with the substance of interest.
As used herein, the term "reaction site" is a localized region
where a desired reaction may occur. A reaction site may include
support surfaces of a substrate where a substance may be
immobilized thereon. For example, a reaction site may include a
substantially planar surface in a channel of a flow cell that has a
colony of clonally amplified sstDNA thereon. Furthermore, a
plurality of reactions sites may be arranged side-by-side in a
matrix, such as in microarrays. A reaction site can also include a
reaction chamber that at least partially defines a spatial region
or volume configured to compartmentalize the desired reaction. As
used herein, the term "reaction chamber" includes a spatial region
that is in fluid communication with a flow channel. The reaction
chamber may be at least partially separated from the surrounding
environment or other spatial regions. For example, a plurality of
reaction chambers may be separated from each other by shared walls.
As a more specific example, the reaction chamber may include a
cavity defined by interior surfaces of a well and have an opening
or aperture so that the cavity may be in fluid communication with a
flow channel.
In some embodiments, the reaction chambers are sized and shaped
relative to solids (including semi-solids) so that the solids may
be inserted, fully or partially, therein. For example, the reaction
chamber may be sized and shaped to accommodate only one capture
bead. The capture bead may have clonally amplified DNA or other
substances thereon. Alternatively, the reaction chamber may be
sized and shaped to receive an approximate number of beads or solid
substrates. As another example, the reaction chambers may also be
filled with a porous gel or substance that is configured to control
diffusion or filter fluids that may flow into the reaction
chamber.
As used herein, a "substance" includes items or solids, such as
capture beads, as well as biological or chemical substances. As
used herein, a "biological or chemical substance" includes
biomolecules, samples of interest, and other chemical compound(s).
A biological or chemical substance may be used to detect, identify,
or analyze other chemical compound(s), or function as
intermediaries to study or analyze other chemical compound(s). In
particular embodiments, the biological or chemical substances
include a biomolecule. As used herein, a "biomolecule" includes at
least one of nucleosides, nucleic acids, polynucleotides,
oligonucleotides, proteins, enzymes, polypeptides, antibodies,
antigens, ligands, receptors, polysaccharide, carbohydrate,
polyphosphates cells, tissues, organisms, and any other
biologically active chemical compound(s) such as analogs or
mimetics of the aforementioned species.
In a further example, a biological or chemical substance or a
biomolecule includes an enzyme or reagent used in a coupled
reaction to detect the product of another reaction such as an
enzyme or reagent used to detect pyrophosphate in a pyrosequencing
reaction. Enzymes and reagents useful for pyrophosphate detection
are described, for example, in U.S. Patent Publication No.
2005/0244870 A1, which is incorporated herein in its entirety.
Biomolecules, samples, and biological or chemical substances may be
naturally occurring or synthetic and may be suspended in a solution
or mixture within a spatial region. Biomolecules, samples, and
biological or chemical substances may also include a pharmaceutical
composition. In some cases, biomolecules, samples, and biological
or chemical substances of interest may be referred to as targets,
probes, or analytes.
As used herein, a "microdevice" and a "biosensor cartridge" include
a structure having a plurality of the reaction sites. A microdevice
or a biosensor cartridge may include at least one of a flow channel
and an electrical circuit. For example, a microdevice or a
biosensor cartridge may include at least one flow channel that is
in fluid communication with the reaction sites. As such, the
microdevice or biosensor cartridge may be referred to as a
microfluidic device. In some embodiments, the biosensor cartridge
includes a microdevice. For example, after the microdevice is
prepared or manufactured, the microdevice may be coupled to a
housing or container to form the biosensor cartridge. In some
embodiments, the microdevices and the biosensor cartridges may be
self-contained, disposable units. However, other embodiments may
include an assembly with removable parts that allow a user to
access an interior of the microdevice for maintenance or
replacement of components or samples. The microdevice and the
biosensor cartridge may be removably coupled or engaged to larger
bioassay systems, such as a sequencing system, that conducts
controlled reactions therein.
In particular embodiments, the microdevice or biosensor cartridge
may include an activity detector. As used herein, an "activity
detector" is any device or component that is capable of detecting
the activity that is indicative of a desired reaction. An activity
detector may be able detect predetermined events, properties,
qualities, or characteristics within a predefined volume or area.
For example, an activity detector may be able to capture an image
of the predefined volume or area. An activity detector may be able
detect an ion concentration within a predefined volume of a
solution or along a predefined area. Exemplary activity detectors
include charged-coupled devices (CCD's) (e.g., CCD cameras);
photomultiplier tubes (PMT's); molecular characterization devices
or detectors, such as those used with nanopores; microcircuit
arrangements, such as those described in U.S. Pat. No. 7,595,883,
which is incorporated herein by reference in the entirety; and
CMOS-fabricated sensors having field effect transistors (FET's),
including chemically sensitive field effect transistors (chemFET),
ion-sensitive field effect transistors (ISFET), and/or metal oxide
semiconductor field effect transistors (MOSFET).
However, in other embodiments, the microdevice or biosensor
cartridge does not include the activity detector. Such microdevices
or biosensor cartridges may include flow cells that are configured
to be positioned adjacent to an activity detector. For example, the
microdevice may be a flow cell that is positioned directly adjacent
to a CCD camera.
As used herein, when the terms "removably" and "coupled" (or
"engaged") are used together to describe a relationship between the
microdevice (or biosensor cartridge) and a system receptacle or
interface of a bioassay system, the term is intended to mean that a
connection between the microdevice and the system receptacle is
readily separable without destroying the system receptacle.
Accordingly, the microdevice may be removably coupled or engaged to
the system receptacle in an electrical manner such that the mating
contacts of the bioassay system are not destroyed. The microdevice
may be removably coupled or engaged to the system receptacle in a
mechanical manner such that the features that hold the microdevice
are not destroyed. The microdevice may be removably coupled or
engaged to the system receptacle in a fluidic manner such that the
ports of the system receptacle are not destroyed. The system
receptacle or a component is not considered to be "destroyed," for
example, if only a simple adjustment to the component (e.g.,
realigning) or a simple replacement (e.g., replacing a nozzle) is
required. However, in other embodiments where noted, the
microdevice and the system receptacle may be readily separable
without destroying either the microdevice or the system receptacle.
Components are readily separable when the components may be
separated from each other without undue effort or a significant
amount of time spent in separating the components.
As used herein, the term "fluid communication" or "fluidicly
coupled" refers to two spatial regions being connected together
such that a liquid or gas may flow between the two spatial regions.
For example, a microfluidic channel may be in fluid communication
with a reaction chamber such that a fluid may flow freely into the
reaction chamber from the microfluidic channel. The terms "in fluid
communication" or "fluidicly coupled" allow for two spatial regions
being in fluid communication through one or more valves,
restrictors, or other fluidic components that are configured to
control or regulate a flow of fluid through a system. In some
cases, two spatial regions may be in fluid communication with each
other even if, under certain conditions, a certain fluid would not
be able to flow freely into a spatial region. For example, although
a reaction chamber may be in fluid communication with a flow
channel if the fluid were an aqueous solution, the interior
surfaces of the reaction chamber may be modified or have certain
properties that prevent the fluid from flowing into the reaction
chamber when the fluid is a non-polar solution. For instance, the
fluid may be oil and the interior surfaces of the reaction chamber
may be hydrophilic.
As used herein, the term "immobilized," when used with respect to a
biomolecule or biological or chemical substance, includes
substantially attaching the biomolecule or biological or chemical
substance at a molecular level to a surface. For example,
biomolecule or biological or chemical substance may be immobilized
to a surface of the substrate material using adsorption techniques
including non-covalent interactions (e.g., electrostatic forces,
van der Waals, and dehydration of hydrophobic interfaces) and
covalent binding techniques where functional groups or linkers
facilitate attaching the biomolecules to the surface. Immobilizing
biomolecules or biological or chemical substances to a surface of a
substrate material may be based upon the properties of the
substrate surface, the liquid medium carrying the biomolecule or
biological or chemical substance, and the properties of the
biomolecules or biological or chemical substances themselves. In
some cases, a substrate surface may be first modified to have
functional groups bound to the surface. The functional groups may
then bind to biomolecules or biological or chemical substances to
immobilize them thereon.
In some embodiments, nucleic acids can be attached to a surface and
amplified using bridge amplification. Useful bridge amplification
methods are described, for example, in U.S. Pat. No. 5,641,658;
U.S. Patent Publ. No. 2002/0055100 A1; U.S. Pat. No. 7,115,400;
U.S. Patent Publ. No. 2004/0096853 A1; U.S. Patent Publ. No.
2004/0002090 A1; U.S. Patent Publ. No. 2007/0128624 A1; and U.S.
Patent Publ. No. 2008/0009420 A1, each of which is incorporated
herein in its entirety. Another useful method for amplifying
nucleic acids on a surface is rolling circle amplification (RCA),
for example, using methods set forth in further detail below.
In particular embodiments, the assay protocols executed by the
systems and methods described herein include the use of natural
nucleotides and also enzymes that are configured to interact with
the natural nucleotides. Natural nucleotides include, for example,
ribonucleotides or deoxyribonucleotides. Natural nucleotides can be
in the mono-, di-, or tri-phosphate form and can have a base
selected from adenine (A), Thymine (T), uracil (U), guanine (G) or
cytosine (C). It will be understood however that non-natural
nucleotides or analogs of the aforementioned nucleotides can be
used. Some examples of useful non-natural nucleotides are set forth
below in regard to reversible terminator-based sequencing by
synthesis methods.
In some embodiments, items or solid substances (including
semi-solid substances) may be disposed within the reaction
chambers. When disposed, the item or solid may be physically held
or immobilized within the reaction chamber through an interference
fit, adhesion, or entrapment. Exemplary items or solids that may be
disposed within the reaction chambers include polymer beads,
pellets, agarose gel, powders, quantum dots, or other solids that
may be compressed and/or held within the reaction chamber. In
particular embodiments, a nucleic acid superstructure, such as a
DNA ball, can be disposed in or at a reaction chamber, for example,
by attachment to an interior surface of the reaction chamber or by
residence in a liquid within the reaction chamber. A DNA ball or
other nucleic acid superstructure can be preformed and then
disposed in or at the reaction chamber. Alternatively, a DNA ball
can be synthesized at the reaction chamber. A DNA ball can be
synthesized by rolling circle amplification to produce a concatamer
of a particular nucleic acid sequence and the concatamer can be
treated with conditions that form a relatively compact ball. DNA
balls and methods for their synthesis are described, for example
in, U.S. Patent Publ. Nos. 2008/0242560 A1 or 2008/0234136 A1, each
of which is incorporated herein in its entirety.
A substance that is held or disposed in a reaction chamber can be
in a solid, liquid, or gaseous state. A substance can be held in a
reaction chamber in the same state that it was introduced to the
reaction chamber. For example, a liquid substance can be loaded
into a reaction chamber and the substance can remain liquid whether
or not it is converted to a different chemical species.
Alternatively, a substance can be introduced to a reaction chamber
in a first state and then converted to another state.
As used herein, an "environment" may be liquid, gas, or solid or a
combination thereof. The environments in the reaction chambers and
the flow channel may be different. As used herein, when the terms
"separate" or "isolate" are used with respect to a surrounding
environment and a substance within a reaction chamber, the
substance may be separate from the surrounding environment without
being completely isolated from the surrounding environment. For
instance, a fluid in the flow channel may interface with, but not
substantially intermix with through diffusion and the like, the
environment or substance in the reaction chamber. By way of a more
specific example, a hydrophilic solution within the reaction
chamber may interface with a non-polar liquid that flows through
the flow channel. In alternative embodiments, separation of a
substance from a surrounding environment can be a fluidic isolation
such that the substance in the reaction chamber is prevented from
making physical contact with the surrounding environment. For
example, a reaction chamber may be capped or sealed.
The reaction chambers and flow channels may have microfluidic
dimensions in which surface tension and cohesive forces of a liquid
in the reaction chamber and the adhesive forces between the liquid
and interior surfaces that define the reaction chamber can have a
significant effect on the liquid therein. As understood by those
skilled in the art, a liquid may have different wetting abilities
to a solid surface depending upon the natures of the liquid and the
solid surface. Wetting is a liquid's ability to spread along a
solid surface. The wetting of a solid surface by a liquid is
controlled by the intermolecular interactions of molecules along an
interface between the two phases. If the adhesive forces are
relatively greater than the cohesive forces, the wetting of the
liquid to the surface is greater. If the cohesive forces are
relatively greater than the adhesive forces, the wetting of the
liquid to the surface is smaller. Embodiments may utilize the
wetting abilities of a fluid during the course of an assay or other
usage.
In embodiments utilizing aqueous or polar liquids, the interaction
between the liquid and the solid surface can be characterized as
hydrophobic or hydrophilic. As used herein, a solid surface is
hydrophobic if it repels an aqueous or polar liquid. For example, a
contact angle between the aqueous or polar liquid and the
hydrophobic surface of the solid is typically greater than 90
degrees. A surface is hydrophilic if it is attracted to an aqueous
or polar liquid. For example, a contact angle between the aqueous
or polar liquid and the hydrophilic surface of the solid will
typically be less than 90 degrees.
In other embodiments, a non-polar liquid, such as alkanes, oils,
and fats, may be used as the liquid within the reaction chamber
and/or as part of the surrounding environment. Non-polar liquids
may be attracted to a surface that has a hydrophobic interaction
with aqueous or polar liquids. Likewise, non-polar liquids are not
attracted to a surface that has a hydrophilic interaction with
aqueous or polar liquids. As such, hydrophobic and hydrophilic
surfaces may be used with embodiments described herein to control
the flow of liquids through portions of the flow channel or within
the reaction chambers.
Other factors may affect the contact angle or the wetting of a
liquid to a solid. For example, a purity of the liquid or whether a
surfactant is used may affect the surface tension of the liquid and
the molecular interactions along the solid-liquid interface. A
purity of the solid or whether a coating is placed on the solid
surface may affect the surface energy of a solid. Also, temperature
of the environment, a composition of the surrounding air, and the
roughness or smoothness of the surface may all affect the
interactions between the liquid and the solid surface. As such,
embodiments described herein may utilize these other factors for
certain purposes.
FIG. 1 is a block diagram of a bioassay system 100 for biological
or chemical analysis formed in accordance with one embodiment. The
term "bioassay" is not intended to be limiting as the bioassay
system 100 may operate to obtain any information or data that
relates to at least one of a biological and chemical substance. In
some embodiments, the bioassay system 100 is a workstation that may
be similar to a bench-top device or desktop computer. For example,
a majority of the systems and components for conducting the desired
reactions can be within a common housing 116.
In particular embodiments, the bioassay system 100 is a nucleic
acid sequencing system (or sequencer) configured for various
applications, including de novo sequencing, resequencing of whole
genomes or target genomic regions, and metagenomics. The sequencer
may also be used for RNA analysis. By way of example, the bioassay
system 100 may read, for example, 100,000 beads and at about a 400
bp read length. Furthermore, in some embodiments, the bioassay
system 100 may amplify template nucleic acid before sequencing of
the nucleic acid is initiated.
The bioassay system 100 is configured to interact with a
microdevice (or biosensor cartridge) 102 to perform desired
reactions within the microdevice 102. In particular embodiments,
the bioassay system 100 is configured to perform massively parallel
reactions within the microdevice 102. The microdevice 102 includes
one or more reaction sites where desired reactions can occur. The
reaction sites can be, for example, elongated channels, reaction
chambers, or planar surfaces. The microdevice 102 includes a flow
channel that receives fluid from the bioassay system 100 and
directs the fluid toward the reaction sites. Optionally, the
microdevice 102 is configured to engage a thermal element for
transferring thermal energy into or out of the flow channel.
Furthermore, in some embodiments, the microdevice 102 includes an
activity detector for detecting activity that is indicative of the
occurrence of one or more desired reactions.
The bioassay system 100 may include various components, assemblies,
and systems (or sub-systems) that interact with each other to
perform a predetermined method or assay protocol for biological or
chemical analysis. For example, the bioassay system 100 includes a
system controller 104 that may communicate with the various
components, assemblies, and sub-systems of the bioassay system 100
and also the microdevice 102. The bioassay system 100 may also
include a system receptacle or interface 112 that engages the
microdevice 102; a fluidic control system 106 to control the flow
of fluid throughout a fluid network of the bioassay system 100 and
the microdevice 102; a fluid storage system 108 that is configured
to hold all fluids that may be used by the bioassay system; and a
temperature control system 110 that may regulate the temperature of
the fluid in the fluid network, the fluid storage system 108,
and/or the microdevice 102.
Also shown, the bioassay system 100 may include a user interface
114 that interacts with the user. For example, the user interface
114 may include a display 113 to display or request information
from a user and a user input device 115 to receive user inputs. In
some embodiments, the display 113 and the user input device 115 are
the same device (e.g., touchscreen). As will be discussed in
greater detail below, the bioassay system 100 may communicate with
various components to perform the desired reactions. The bioassay
system 100 may also be configured to analyze the detection data to
provide a user with desired information.
The system controller 104 may include any processor-based or
microprocessor-based system, including systems using
microcontrollers, reduced instruction set computers (RISC),
application specific integrated circuits (ASICs), field
programmable gate array (FPGAs), logic circuits, and any other
circuit or processor capable of executing functions described
herein. The above examples are exemplary only, and are thus not
intended to limit in any way the definition and/or meaning of the
term system controller. In the exemplary embodiment, the system
controller 104 executes a set of instructions that are stored in
one or more storage elements, memories, or modules in order to at
least one of obtain and analyze detection data. Storage elements
may be in the form of information sources or physical memory
elements within the bioassay system 100.
The set of instructions may include various commands that instruct
the bioassay system 100 or microdevice 102 to perform specific
operations such as the methods and processes of the various
embodiments described herein. The set of instructions may be in the
form of a software program. As used herein, the terms "software"
and "firmware" are interchangeable, and include any computer
program stored in memory for execution by a computer, including RAM
memory, ROM memory, EPROM memory, EEPROM memory, and non-volatile
RAM (NVRAM) memory. The above memory types are exemplary only, and
are thus not limiting as to the types of memory usable for storage
of a computer program.
The software may be in various forms such as system software or
application software. Further, the software may be in the form of a
collection of separate programs, or a program module within a
larger program or a portion of a program module. The software also
may include modular programming in the form of object-oriented
programming. After obtaining the detection data, the detection data
may be automatically processed by the bioassay system 100,
processed in response to user inputs, or processed in response to a
request made by another processing machine (e.g., a remote request
through a communication link).
The system controller 104 may be connected to the microdevice 102
and the other components of the bioassay system 100 via
communication links. The system controller 104 may also be
communicatively connected to off-site systems or servers. The
communication links may be hardwired or wireless. The system
controller 104 may receive user inputs or commands, from the user
interface 114. The user input device 115 may include a keyboard,
mouse, a touch-screen panel, and/or a voice recognition system, and
the like. Alternatively or in addition, the user input device 115
may also be the display 113.
The fluidic control system 106 includes a fluid network and is
configured to direct and regulate the flow of one or more fluids
through the fluid network. The fluid network may be in fluid
communication with the microdevice 102 and the fluid storage system
108. For example, select fluids may be drawn from the fluid storage
system 108 and directed to the microdevice 102 in a controlled
manner, or the fluids may be drawn from the microdevice 102 and
directed toward, for example, a waste reservoir in the fluid
storage system 108. Although not shown, the fluidic control system
106 may include flow sensors that detect a flow rate or pressure of
the fluids within the fluid network. The sensors may communicate
with the system controller 104.
The temperature control system 110 is configured to regulate the
temperature of fluids at different regions of the fluid network,
the fluid storage system 108, and/or the microdevice 102. For
example, the temperature control system 110 may include a
thermocycler that interfaces with the microdevice 102 and controls
the temperature of the fluid that flows along the reaction sites in
the microdevice 102. The temperature control system 110 may also
regulate the temperature of solid elements or components of the
bioassay system 100 or the microdevice 102. Although not shown, the
temperature control system 110 may include sensors to detect the
temperature of the fluid or other components. The sensors may
communicate with the system controller 104.
The fluid storage system 108 is in fluid communication with the
microdevice 102 and may store various reaction components or
reactants that are used to conduct the desired reactions therein.
The fluid storage system 108 may also store fluids for washing or
cleaning the fluid network and microdevice 102 and for diluting the
reactants. For example, the fluid storage system 108 may include
various reservoirs to store reagents, enzymes, other biomolecules,
buffer solutions, aqueous, and non-polar solutions, and the like.
Furthermore, the fluid storage system 108 may also include waste
reservoirs for receiving waste products from the microdevice
102.
The system receptacle or interface 112 is configured to engage the
microdevice 102 in at least one of a mechanical, electrical, and
fluidic manner. The system receptacle 112 may hold the microdevice
102 in a desired orientation to facilitate the flow of fluid
through the microdevice 102. The system receptacle 112 may also
include electrical contacts that are configured to engage the
microdevice 102 so that the bioassay system 100 may communicate
with the microdevice 102 and/or provide power to the microdevice
102. Furthermore, the system receptacle 112 may include fluidic
ports (e.g., nozzles) that are configured to engage the microdevice
102. In some embodiments, the microdevice 102 is removably coupled
to the system receptacle 112 in a mechanical manner, in an
electrical manner, and also in a fluidic manner.
In some embodiments, the bioassay system 100 may have
interchangeable or swappable devices (e.g., plug-and-play). For
example, the system receptacle 112 may be readily replaced or
substituted with a different system receptacle. This may occur when
a different type of microdevice 102 is desired to be used.
Furthermore, the fluid storage system 108 may be a container that
is readily separated from the fluid network and replaced by another
container. This may occur when the fluid in the container is
depleted, has expired, or a different container is required because
a user of the bioassay system 100 desires to run a different assay
protocol. Furthermore, the system controller 104 may have swappable
devices (e.g., if the user desires to use the bioassay system 100
to execute a different assay protocol).
In addition, the bioassay system 100 may communicate remotely with
other systems or networks. Detection data obtained by the bioassay
system 100 may be stored in a remote database.
FIG. 2 is a block diagram of the system controller 104 in the
exemplary embodiment. In one embodiment, the system controller 104
includes one or more processors or modules that can communicate
with one another. The system controller 104 is illustrated
conceptually as a collection of modules, but may be implemented
utilizing any combination of dedicated hardware boards, DSPs,
processors, etc. Alternatively, the system controller 104 may be
implemented utilizing an off-the-shelf PC with a single processor
or multiple processors, with the functional operations distributed
between the processors. As a further option, the modules of
described below may be implemented utilizing a hybrid configuration
in which certain modular functions are performed utilizing
dedicated hardware, while the remaining modular functions are
performed utilizing an off-the-shelf PC and the like. The modules
also may be implemented as software modules within a processing
unit.
During operation, a communication link 120 may transmit commands to
or receive data from the microdevice 102 (FIG. 1) and/or the
sub-systems 106, 108, 110 (FIG. 1). A communication link 122 may
receive user input from the user interface 114 (FIG. 1) and
transmit data or information to the user interface 114. Data from
the microdevice 102 or sub-systems 106, 108, 110 may be processed
by the system controller 104 in real-time during a bioassay
session. Additionally or alternatively, data may be stored
temporarily in a system memory during a bioassay session and
processed in less than real-time or off-line operation.
The system controller 104 may include a plurality of modules
131-138 that communicate with a main control module 130. The main
control module 130 may communicate with the user interface 114
(FIG. 1). Although the modules 131-138 are shown as communicating
directly with the main control module 130, the modules 131-138 may
also communicate directly with each other, the user interface 114,
and the microdevice 102. Also, the modules 131-138 may communicate
with the main control module 130 through the other modules.
The plurality of modules 131-138 include system modules 131-133
that communicate with the sub-systems 106, 108, and 110,
respectively. The fluidic control module 131 may communicate with
the fluidic control system 106 to control the valves and flow
sensors of the fluid network for controlling the flow of one or
more fluids through the fluid network. The fluid storage module 132
may notify the user when fluids are low or when the waste reservoir
must be replaced. The fluid storage module 132 may also communicate
with the temperature control module 133 so that the fluids may be
stored at a desired temperature.
The plurality of modules 131-138 may also include a device module
134 that communicates with the microdevice 102 and an
identification module 135 that determines identification
information relating to the microdevice 102. The device module 134
may, for example, communicate with the system receptacle 112 to
confirm that the microdevice has established an electrical and
fluidic connection with the bioassay system 100. The identification
module 135 may receive signals that identify the microdevice 102.
The identification module 135 may use the identity of the
microdevice 102 to provide other information to the user. For
example, the identification module 135 may determine and then
display a lot number, a date of manufacture, or a protocol that is
recommended to be run with the microdevice 102.
The plurality of modules 131-138 may also include a detection data
analysis module 138 that receives and analyzes the detection data
(e.g., image data) from the microdevice 102. The processed
detection data may be stored for subsequent analysis or may be
transmitted to the user interface 114 to display desired
information to the user.
Protocol modules 136 and 137 communicate with the main control
module 130 to control the operation of the sub-systems 106, 108,
and 110 when conducting predetermined assay protocols. The protocol
modules 136 and 137 may include sets of instructions for
instructing the bioassay system 100 to perform specific operations
pursuant to predetermined protocols. The protocol modules 136 and
137 include a sequencing-by-synthesis (SBS) module 136 that may be
configured to issue various commands for performing
sequencing-by-synthesis processes. In some embodiments, the SBS
module 136 may also process detection data.
By way of one example, the SBS module 136 may be configured to
issue various commands for performing the steps of a pyrosequencing
protocol. In this case, the microdevice 102 may include millions of
wells where each well has a single capture bead having clonally
amplified sstDNA thereon. Each well may also include other smaller
beads that, for example, may carry immobilized enzymes (e.g., ATP
sulfurylase and luciferase) or facilitate holding the capture bead
in the well. The SBS module 136 may be configured to issue commands
to the fluidic control module 106 to run consecutive cycles of
fluids that carry a single type of nucleotide (e.g., 1st cycle: A;
2nd cycle: G; 3rd cycle: C; 4th cycle: T; 5th cycle: A; 6th cycle:
G; 7th cycle: C; 8th cycle: T; and on). When a nucleotide is
incorporated into the DNA, pyrophosphate is released thereby
instigating a chain reaction where a burst of light is generated.
The burst of light may be detected by an activity detector.
Detection data may be communicated to the main control module 130,
the detection data analysis module 138, and/or the SBS module 136
for processing. The detection data may be stored for later analysis
or may be analyzed by the system controller 104 and an image may be
sent to the user interface 114.
The SBS module 136 may also be configured to issue commands for
other sequencing-by-synthesis processes. For example, the SBS
module 136 may issue commands to perform bridge PCR where clusters
of clonal amplicons are formed on localized areas within a channel
(or lane) of a flow cell. After generating the amplicons through
bridge PCR, the amplicons may be "linearized" to make sstDNA and a
sequencing primer may be hybridized to a universal sequence that
flanks a region of interest. For example, a reversible
terminator-based sequencing by synthesis method can be used as
follows. Each sequencing cycle extends the sstDNA by a single base
and is accomplished by modified DNA polymerase and a mixture of
four types of nucleotides. The different types of nucleotides can
have unique fluorescent labels, and each nucleotide can further
have a reversible terminator that allows only a single-base
incorporation to occur in each cycle. After a single base is added
to the sstDNA, an image in four channels is taken (i.e., one for
each fluorescent label). After imaging, the fluorescent label and
the terminator are chemically cleaved from the sstDNA. Another
similar sequencing cycle may follow. In such a sequencing protocol,
the SBS module 136 may instruct the fluidic control system 106 to
direct a flow of reagent and enzyme solutions through the
microdevice 102. Exemplary reversible terminator-based SBS methods
which can be utilized with the apparatus and methods set forth
herein are described in US Patent Application Publication No.
2007/0166705 A1, US Patent Application Publication No. 2006/0188901
A1, U.S. Pat. No. 7,057,026, US Patent Application Publication No.
2006/0240439 A1, US Patent Application Publication No. 2006/0281109
A1, PCT Publication No. WO 05/065814, US Patent Application
Publication No. 2005/0100900 A1, PCT Publication No. WO 06/064199
and PCT Publication No. WO 07/010251, each of which is incorporated
herein by reference in its entirety. Exemplary reagents for
reversible terminator-based SBS are described in U.S. Pat. No.
7,541,444; U.S. Pat. No. 7,057,026; U.S. Pat. No. 7,414,116; U.S.
Pat. No. 7,427,673; U.S. Pat. No. 7,566,537; U.S. Pat. No.
7,592,435 and WO 07/135368, each of which is incorporated herein by
reference in its entirety.
The plurality of protocol modules may also include an amplification
module 137 that is configured to issue commands to the fluidic
control system 106 and the temperature control system 110 for
amplifying a product within the microdevice 102. For example, the
microdevice 102 may be engaged to the bioassay system 100. The
bioassay system 100 may identify the type of microdevice or other
information and automatically run an amplification protocol.
Alternatively, the bioassay system 100 may request additional
information from the user. The amplification module 137 may issue
instructions to the fluidic control system 106 to deliver necessary
amplification components to reaction chambers within the
microdevice 102. The reaction chambers may already contain some
components for amplification, such as the template DNA and/or
primers. After delivering the amplification components to the
reaction chambers, the amplification module 137 may instruct the
temperature control system 110 to cycle through different
temperature stages according to known amplification protocols.
In some embodiments, the amplification and SBS modules may operate
in a single assay protocol where, for example, template nucleic
acid is amplified and subsequently sequenced within the same
biosensor cartridge.
In some embodiments, the user may provide user inputs through the
user interface 114 to select an assay protocol to be run by the
bioassay system 100. In other embodiments, the bioassay system 100
may automatically detect the type of microdevice 102 that has been
inserted into the system receptacle 112 and confirm with the user
the assay protocol to be run. Alternatively, the bioassay system
100 may offer a limited number of assay protocols that could be run
with the determined type of microdevice 102. The user may select
the desired assay protocol, and the bioassay system 100 may then
perform the selected assay protocol based on preprogrammed
instructions.
However, the bioassay system 100 may also allow the user to
reconfigure an assay protocol. After determining the assay protocol
to run, the bioassay system 100 may offer options to the user
through the user interface 114 for modifying the determined
protocol. For example, if it is determined that the microdevice 102
is to be used for amplification, the bioassay system 100 may
request a temperature for the annealing cycle. Furthermore, the
bioassay system 100 may issue warnings to a user if a user has
provided user inputs that are generally not acceptable for the
selected assay protocol.
FIG. 3 is a block diagram of an exemplary workstation 200 for
biological or chemical analysis in accordance with one embodiment.
The workstation 200 may have similar features, systems, and
assemblies as the bioassay system 100 described above. For example,
the workstation 200 may have a fluidic control system, such as the
fluidic control system 106 (FIG. 1), that is fluidicly coupled to a
biosensor cartridge or microdevice 235 through a fluid network 238.
The fluid network 238 may include a reagent cartridge 240, a valve
block 242, a main pump 244, a debubbler 246, a 3-way valve 248, a
flow restrictor 250, a waste removal system 252, and a purge pump
254. In particular embodiments, most of the components or all of
the components describe above are within a common workstation
housing 230 (FIG. 4).
A flow of fluid is indicated by arrows along the fluid network 238.
For example, reagent solutions may be removed from the reagent
cartridge 240 and flow through the valve block 242. The valve block
242 may facilitate creating a zero-dead volume of the fluid flowing
to the biosensor cartridge 235 from the reagent cartridge 240. The
valve block 242 can select or permit one or more liquids within the
reagent cartridge 240 to flow through the fluid network 238. For
example, the valve block 242 can include 16 solenoid valves that
have a compact arrangement. Each solenoid valve can control the
flow of a fluid from a single reservoir bag. In some embodiments,
the valve block 242 can permit two or more different liquids to
flow into the fluid network 238 at the same time thereby mixing the
two or more different liquids. After leaving the valve block 242,
the fluid may flow through the main pump 244 and to the debubbler
246. The debubbler 246 is configured to remove unwanted gases that
have entered or been generated within the fluid network 238.
From the debubbler 246, fluid may flow to the 3-way valve 248 where
the fluid is either directed to the biosensor cartridge 235 or
bypassed to the waste removal system 252. A flow of the fluid
within the biosensor cartridge 235 may be at least partially
controlled by the flow restrictor 250 located downstream from the
biosensor cartridge 235. Furthermore, the flow restrictor 250 and
the main pump 244 may coordinate with each other to control the
flow of fluid across reaction sites and/or control the pressure
within fluid network 238. Fluid may flow through the biosensor
cartridge 235 and onto the waste removal system 252. Optionally,
fluid may flow through the purge pump 254 and into, for example, a
waste reservoir bag within the reagent cartridge 240.
Also shown in FIG. 3, the workstation 200 may include a temperature
control system, such as the temperature control system 110, that is
configured to regulate or control a thermal environment of the
different components and sub-systems of the workstation 200. The
temperature control system 110 can include a reagent cooler 264
that is configured to control a temperature of various fluids used
by the workstation 200, and a thermocycler 266 that is configured
to control a temperature of the biosensor cartridge 235. The
thermocycler 266 can include a thermal element (not shown) that
interfaces with the biosensor cartridge.
Furthermore, the workstation 200 may include a system controller or
SBS board 260 that may have similar features as the system
controller 104 described above. The SBS board 260 may communicate
with the various components and sub-systems of the workstation 200
as well as the biosensor cartridge 235. Furthermore, the SBS board
260 may communicate with remote systems to, for example, store data
or receive commands from the remote systems. The workstation 200
may also include a touch screen user interface 262 that is
operatively coupled to the SBS board 260 through a single-board
computer (SBC) 272. The workstation 200 may also include a
compact-flash (CF) drive and/or a hard drive 270 for storing user
data in addition to other software.
FIG. 4 provides various perspective views of the workstation 200.
In particular embodiments, the workstation 200 is a stand-alone or
bench-top unit such that all of the components described above with
respect to FIG. 3 may be held within the workstation housing 230.
However, in other embodiments, the workstation housing 230 may
contain or partially contain only some of the components. The
workstation 200 permits a user to perform desired reactions within
the biosensor cartridge 235 (FIG. 3) and, optionally, perform
primary analysis of obtained detection data of the desired
reactions. The primary analysis may, for example, indicate to the
user that the assay protocol was successfully run and provide
preliminary results of the assay protocol. The user interface 262
may be configured to receive user inputs and commands as well as
display information to the user. Also shown, the workstation 200
may also include a system receptacle 212 that is configured to
receive and engage the biosensor cartridge 235.
FIGS. 5 and 6 illustrate a biosensor cartridge 300 formed in
accordance with one embodiment that may be used with a bioassay
system or workstation, such as the bioassay system 100 (FIG. 1) and
the workstation 200 (FIG. 3). FIG. 5 is a partially exploded
perspective view, and FIG. 6 provides plan views of opposite side
surfaces 314 and 315 of the biosensor cartridge 300. As shown, the
biosensor cartridge 300 is oriented with respect to a vertical or
elevational axis 392 (FIG. 5) and lateral axes 390 and 391. In the
illustrated embodiment, the biosensor cartridge 300 may include a
microdevice 302. The biosensor cartridge 300 may also have a
housing or casing 304 that encloses at least a portion of the
microdevice 302. In the illustrated embodiment, the casing 304 may
include opposite shells 306 and 308 that couple to each other along
an interface. In some embodiments, the shells 306 and 308 are
readily separated thereby allowing a user or a machine to replace
components within the casing 304, such as the microdevice 302. For
example, the shells 306 and 308 may form an interference fit (e.g.,
snap-fit) or slidably engage each other in a locking arrangement.
The shells 306 and 308 may also use fasteners (e.g., screws or
plugs) that removably couple the shells 306 and 308 together.
As shown, each of the shells 306 and 308 includes an opening or
window 310 and 312 (FIG. 6), respectively, that is sized and shaped
to provide access to the microdevice 302 therein or permit the
microdevice 302 to project therethrough. As shown in FIG. 6, when
the shells 306 and 308 are coupled together, the biosensor
cartridge 300 may have exterior side surfaces 314 and 315. In the
illustrated embodiment, the side surfaces 314 and 315 face in
substantially opposite directions. For example, the side surfaces
314 and 315 may both face a direction along the vertical axis
392.
The biosensor cartridge 300 may be sized and shaped to facilitate
handling by a user or machine and for being inserted into the
system receptacle 212 (FIG. 4). For example, the biosensor
cartridge may be substantially rectangular or card-shaped. The
biosensor cartridge 300 may have a width W.sub.1, a length L.sub.1,
and a thickness T.sub.1 (as indicated by the dashed lines in FIG.
5). The width W.sub.1, the length L.sub.1, and the thickness
T.sub.1 along with other features of the casing 304 and the
microdevice 302 may be configured to facilitate orienting the
biosensor cartridge 300 when inserted into the system receptacle
212. The dimensions can be, for example, in a range of 1 cm to 50
cm, 1 cm to 25 cm, 1 cm to 10 cm, 5 cm to 50 cm, 5 cm to 25 cm, 5
cm to 10 cm, 10 cm to 50 cm or 10 cm to 25 cm. For example, the
biosensor cartridge 300 or the casing 304 may have a tail end 348
(FIG. 6) that projects a substantial distance away from the
microdevice 302 to allow a user or machine to grip the biosensor
cartridge 300.
FIG. 31 is a cross-section of the biosensor cartridge 300. As
shown, the microdevice 302 includes a device body 316 having
opposite device side surfaces 330 and 332. The side surface 330 may
be a portion of the side surface 314, and the side surface 332 may
be a portion of the side surface 315. The device body 316 may
include inlet and outlet ports 320 and 322 along the same side
surface 330 of the device body 316. In alternative embodiments, the
inlet and outlet ports 320 and 322 may be on opposite side
surfaces. In other embodiments, at least one of the inlet and
outlet ports 320 and 322 is located on an edge facing in a
direction along the lateral axis 390 or the lateral axis 391 (FIG.
5). Also shown, the inlet and outlet ports 320 and 322 may have
respective openings 321 and 323.
The microdevice 302 can include a flow cell 334 that is mounted to
a base substrate 335. The base substrate 335 may be a printed
circuit, such as a PCB, that includes conductive pathways
therethrough. In alternative embodiments, the base substrate 335 is
only configured to provide structural support to the flow cell 334.
The flow cell 334 and the base substrate 335 may comprise the
device body 316 and form a substantially unitary structure. As
shown, the base substrate 335 comprises a planar body that may have
lateral dimensions that are larger than the lateral dimensions of
the flow cell 334. For example, the base substrate 335 may have a
length L.sub.3, and the flow cell 334 may have a length L.sub.4.
The length L.sub.3 may be greater than the length L.sub.4. When the
flow cell 334 is mounted onto the base substrate 335, the flow cell
334 may be positioned such that the base substrate 335 extends
beyond edges of the flow cell 334. Although not shown, the widths
of the base substrate 335 and the flow cell 334 may be similarly
sized and shaped with respect to each other.
Also shown, the device body 316 can be held within the casing 304
by a frame 317. The frame 317 may be attached to the casing 304 at
the shell 308 or the shell 306. The frame 317 extends around at
least a portion of a perimeter of the device body 316. In
particular embodiments, the frame 317 completely surrounds the
perimeter. The frame 317 may also define a window or opening 350
that is sized and shaped to permit the microdevice 302 (or the flow
cell 334) to extend therethrough. The opening 350 may also block or
prevent the base substrate 335 from moving therethrough. More
specifically, the opening 350 may be defined by an interior edge
352 of the frame 317 and have a length L.sub.6. The length L.sub.6
may be less than the length L.sub.3 of the base substrate 335.
In some embodiments the frame 317 holds the microdevice 302 in a
substantially stationary position with respect to the case 304.
However, in other embodiments, the microdevice 302 may be moveable
or floatable within a restricted space defined by the biosensor
cartridge 300. In such embodiments, the moveable or floatable
quality of the microdevice 302 may permit the microdevice 302 to
align with other components of the workstation 200 to facilitate
fluidicly, thermally, and/or electrically engaging the workstation
200. For example, as shown in FIG. 31, interior surfaces of the
frame 317 and the shell 308 may define a restricted space that has
greater dimensions (e.g., length, height, and width) than the
dimensions of the base substrate 335. In other words, the
restricted space may provide additional spacing between the
interior surfaces of the frame 317 and the shell 308. As such, the
restricted space permits the microdevice 302 to shift and/or
slightly rotate or pivot therein. For example, the microdevice 302
may be moveable in a lateral manner along a plane formed by the
lateral axes 390, 391 (i.e., the microdevice may shift
side-to-side). The microdevice also be moveable in a vertical
manner along the vertical axis 392 (i.e., the microdevice may shift
up-and-down). Furthermore, the microdevice 302 may also rotate or
pivot about a vertical axis that extends through the microdevice
302 and/or rotate or pivot about a lateral axis that extends
through the microdevice 302. Accordingly, the microdevice 302 may
float with respect to the frame 317 or the casing 304.
However, the above description of the floatability of the
microdevice 302 is exemplary only. The microdevice 302 and, more
specifically, the device body 316 may have various structural
features or other configurations that permit the microdevice 302 to
float or move within a restricted space. Furthermore, in other
embodiments, the microdevice 302 is held in a stationary or fixed
position with respect to the casing 304.
Also shown in FIG. 31, the inlet and outlet ports 320 and 322 may
be configured to removably engage nozzles of the workstation 200 to
fluidicly couple a flow channel 327 of the biosensor cartridge 300
to the workstation 200. When in operation, fluid may flow through
the microdevice 302 between the inlet and outlet ports 320 and 322
and respective openings 321 and 323. More specifically, the fluid
may flow along the flow channel 327 within the biosensor cartridge
300 between the inlet and outlet portions 320 and 322. As shown,
the inlet and outlet ports 320 and 322 may be separated from each
other by a spacing 325. The spacing 325 may extend along and
provide access to an engagement area 328 of the common side surface
330. The engagement area 328 may extend along and proximate to the
flow channel within the biosensor cartridge 300.
As will be described in greater detail below, the engagement area
328 may be sized and shaped to interface with a thermal element of
a thermocycler to facilitate controlling a temperature of the fluid
within the microdevice 302. At least a portion of the engagement
area 328 that extends along the flow channel may be a substantially
flat surface. The engagement area 328 may extend along a lateral
plane that is parallel to a plane formed by lateral axes 390 and
391. The side surface 332 may extend parallel to the engagement
area 328.
As shown in FIG. 31, the device body 316 includes port projections
324 and 326 having the inlet and outlet ports 320 and 322. The port
projections 324 and 326 may be separated from each other by the
spacing 325 and the engagement area 328. The port projections 324
and 326 may project away from the casing 304 or the engagement area
328 in a substantially common direction (e.g., in a direction along
the vertical axis 392). When oriented in the system receptacle 212
(FIG. 4), the port projections 324 and 326 may extend substantially
parallel to a gravitational force direction G. The port projections
324 and 326 may permit the flow channel within the biosensor
cartridge 300 to be shaped in a predetermined configuration to
facilitate controlling a flow the fluid therein.
Also shown, the microdevice 302 may also include an array 336 of
electrical mating contacts 338, which may also be referred to as
device contacts or cartridge contacts. The mating contacts 338 may
be located on the side surface 332 such that the fluidic access and
electrical access to the microdevice 302 are provided on opposite
sides of the device body 316 in the illustrated embodiment. The
array 336 may be configured to engage an array of electrical
contacts of the workstation 200 to communicate with the workstation
200. In the illustrated embodiment, the cartridge contacts 338 are
contact pads that interface with the electrical contacts of the
workstation 200. The contact pads may be substantially flush with a
surface of the device side surface 332 to allow the microdevice 302
to slidably engage the workstation 200. However, in alternative
embodiments, the cartridge contacts 338 may be located within
sockets or may have beams or tails that project away from the
device side surface 332. Furthermore, the cartridge contacts 338
may be pogo pins.
To assemble the biosensor cartridge 300, the microdevice 302 may
first be constructed by mounting the flow cell 334 to the base
substrate 335. In the illustrated embodiment, the flow cell 334
includes an activity detector that is communicatively coupled to
electrical circuits within the base substrate 335. The flow cell
334 may be mounted using an adhesive that is sufficient to
withstand the environment in which the microdevice 302 operates.
The microdevice 302 may then be positioned on an interior surface
of the shell 306 such that the array 336 of cartridge contacts 338
is accessible through the window 312. The frame 317 may be mounted
to the shell 308 so that the microdevice 302 is disposed within the
restricted space. Alternatively, the frame 317 may be mounted to
the shell 306 or integrally formed with the shell 306.
As shown, when the shells 306 and 308 are coupled together, the
inlet and outlet ports 320 and 322 and the engagement area 328 are
on a common side surface 314 of the biosensor cartridge 300. The
port projections 324 and 326 may extend through the window 310, and
the array 336 of cartridge contacts 338 may be accessible through
the window 312. Furthermore, the microdevice 302 may be moveable or
floatable with respect to the casing 304.
Although the casing 304 is shown as being constructed from separate
shells 306 and 308, in alternative embodiments, the housing or
casing 304 may be integrally formed with the microdevice 302. For
example, the components that comprise the microdevice 302 may also
form the housing or casing of the biosensor cartridge. Such an
alternative housing or casing may have similar dimensions as the
casing 304 described above. Thus, in some embodiments, the terms
"biosensor cartridge" and "microdevice" may be used
interchangeably.
Returning to FIGS. 5 and 6, the biosensor cartridge 300 may include
an identification component 340 to provide identification
information of the biosensor cartridge 300. The identification
component 340 may facilitate identification, tracking, and sorting
of the biosensor cartridge 300. For example, the identification
information provided by the identification component 340 may be at
least one of an identification number, a date of manufacture, a lot
number, and a type of biosensor cartridge. The identification
information may also relate to the biological or chemical
substances inside the microdevice 302 and identify, for example, a
genome of interest of DNA fragments therein. The identification
information may also provide one or more protocols that may be
executed with the biosensor cartridge 300.
As shown, the identification component 340 may include a label 342
that is affixed to the casing 304. The label 342 may include a
visual indicator 344, such as a bar code. A user or system may scan
the identification component 340 to determine an alpha-numeric code
or some other indicator. The user or system may have access to a
table that includes a listing of codes or other indicators. The
listing may then associate the scanned code or other indicator with
the identification information.
Alternatively or additionally, the identification component 340 may
include a transmitting device 346, such as an RFID tag physically
associated with the biosensor cartridge 300. The transmitting
device 346 may include an integrated circuit for storing and
processing information and/or modulating and demodulating a
radio-frequency (RF) signal. The transmitting device 346 may also
include an antenna for receiving and transmitting the signal. In
such embodiments where the transmitting device is an RFID tag, the
RFID tag may be one of an active RFID tag that has a battery for
transmitting signals autonomously, a passive RFID tags that
requires an external source to provoke signal transmission, and a
battery assisted passive (BAP) RFID tag that requires an external
source to activate the RFID tag.
In some embodiments, the system receptacle 212 and the
identification component 340 may automatically establish a
communication link between each other. For example, the system
receptacle 212 may automatically scan the identification component
340 when the biosensor cartridge 300 is inserted into the system
receptacle 212. The system receptacle 212 may also automatically
receive the identification information from, for example, the
transmitting device 346 when the biosensor cartridge 300 is within
a predetermined distance from the workstation 200. The workstation
200 may then communicate information to the user that relates to
the biosensor cartridge 300. For example, the workstation 200 may
automatically notify the user that the biosensor cartridge 300 has
been inserted into the system receptacle 212. The workstation 200
may then display information on the user interface 214 and/or
automatically prompt the user to select certain options or
features.
FIG. 7 shows a side view of an exemplary microdevice 400 formed in
accordance with one embodiment. The microdevice 400 may be used in
or may form a biosensor cartridge, such as the biosensor cartridge
300. As shown, the microdevice 400 may include a flow cell 402 that
includes a flow cover 404 mounted to sidewalls 406 (only one
sidewall 406 is shown in FIG. 7). The flow cell 402 may also
include a reaction substrate or substrate layer 408. The flow cell
402 may define a flow channel 410 between the substrate layer 408
and the flow cover 404. As shown, the flow cover 404 includes two
inlet channels 411 that are fluidicly coupled to an inlet port (not
shown). Fluid in the flow channel 410 may flow out of the page to
one or more outlet channels that are fluidicly coupled to an outlet
port (not shown).
In some embodiments, the flow cover 404 has an exterior surface 405
that forms an engagement area that is sized and shaped to interface
with a thermal element (not shown) of a thermocycler. The flow
cover 404 may comprise a thermally conductive material that extends
along the flow channel 410. The flow cover 404 may form a cover
wall 413 having a uniform thickness T.sub.2 in portion(s) that
extend along the flow channel 410. As such, thermal energy may more
evenly transfer between a thermal element and the fluid within the
flow channel 410. In some embodiments, the flow cover 404 comprises
a non-transparent material. Optionally, the material may be
transparent in alternative embodiments. The flow cover 404 may be
attached to the sidewalls 406 using one or more attachment
mechanisms. For example, the flow cover 404 may be attached through
an interference fit or by using an adhesive or fastener.
The substrate layer 408 comprises a substrate material that
facilitates conducting desired reactions. As shown, the substrate
layer 408 includes a substrate field 418 that includes a plurality
of reaction sites 412 where desired reactions may occur. In the
illustrated embodiment, the reaction sites 412 are reaction
chambers 414 that each defines a separate spatial region or volume.
The reaction chambers 414 may include apertures 415 that open to
the flow channel 410 so that the corresponding reaction chambers
414 are in fluid communication with the flow channel 410. The
reaction chambers 414 may be sized and shaped for a desired
purpose. For example, the reaction chambers 414 may be sized and
shaped to accommodate a single DNA capture bead, such as those used
in known pyrosequencing protocols. In addition to the DNA bead, the
reaction chambers 414 may hold smaller packing beads and/or beads
having reagents and enzymes immobilized thereon.
However, in alternative embodiments, the reaction sites are not
required to be spatially or physically separated from each other.
For example, reaction sites may be located on a planar surface in a
predetermined manner (e.g., rows and columns of reactions sites)
where each reaction site comprises a portion of the planar surface.
Examples of such arrangements may be found on a microarray. In
other embodiments, reaction sites may be located on a surface of an
elongated channel. The reaction sites may include randomly located
clusters or colonies of biomolecules that are immobilized on the
surface. As such, the reaction sites may be areas along a surface
in addition to spatial regions defined by reaction chambers.
The microdevice 400 may also include an activity detector 420 that
is coupled to the flow cell 402. The activity detector 420 is
configured to detect activity that is indicative of one or more
desired reactions occurring within the microdevice 400. The
activity detector 420 includes an array 425 of pixels 424 that are
configured to detect activity indicative of a desired reaction from
within or along the substrate layer 408. In some embodiments, a
pixel area of each pixel 424 is less than about 50 microns. In more
particular embodiments, the pixel area is less than about 10
microns. An average read noise of each pixel 424 may be, for
example, less than about 150 electrons. In more particular
embodiments, the read noise may be less than about 5 electrons. The
resolution of the array 425 may be greater than about 0.5 Mpixels.
In more specific embodiments, the resolution of the array 425 may
be greater than about 5 Mpixels and, more particularly, greater
than about 10 Mpixels.
The array 425 of pixels 424 may have a fixed position relative to
the substrate field 418. As shown in FIG. 7, the array 425
comprises sub-arrays 426 of pixels 424 in which the sub-arrays 426
are configured to detect activity from a corresponding one reaction
chamber 414. In the illustrated embodiment, the activity detector
420 is affixed to the substrate layer 408. Optionally, the activity
detector 420 and the substrate layer 408 may be attached to each
other through an intermediate layer 422. The intermediate layer 422
may comprise a material or have features that permit the pixels 424
to detect the activity indicative of the desired reaction.
In the illustrated embodiment, the activity detector 420 includes a
microcircuit arrangement, such as the microcircuit arrangement
described in U.S. Pat. No. 7,595,883, which is incorporated herein
by reference in the entirety. More specifically, the activity
detector 420 may comprise an integrated circuit having a planar
array of photodetectors (i.e., the pixels 424) arranged on a side
428 of a detector substrate 430. The photodetectors may be
configured to detect light signals that are emitted from within the
reaction chambers 414. The side 428 may interface with the
substrate layer 408. Circuitry formed within the detector substrate
430 may be configured for at least one of signal amplification,
digitization, storage, and processing. The circuitry may collect
and analyze the detected activity and generate signals for
communicating detection data to a bioassay system. The signals may
be transmitted through electrical contacts of the microdevice 400
or a biosensor cartridge, such as the cartridge contacts 338 (FIG.
6). The circuitry may also perform additional analog and/or digital
signal processing. As such, the array 425 of pixels 424 may be
communicatively coupled to the electrical contacts that interface
with a bioassay system. Furthermore, the circuitry may also include
an identification component or module that is configured to provide
identification information to the bioassay system.
FIGS. 8-10 illustrate exemplary activity detectors in greater
detail. FIG. 8 is a perspective view of a portion of the substrate
field 418. At least a portion of the intermediate layer 422 (FIG.
7) may include wire-bonding for attaching the substrate layer 408
(FIG. 7) to the side 428 of the activity detector 420. The
substrate layer 408 may be deposited onto the wire-bonding of the
intermediate layer 422. The substrate layer 408 may comprise a
polymer material, such as SUB. In the illustrated embodiment, the
reaction chambers 414 have a predetermined pattern along the
substrate layer 408 (i.e., the reaction chambers 414 form an
array). For example, as shown in FIG. 8, the reaction chambers 414
may have a regular hexagonal-shape cross-section and form a
honeycomb-like lattice along the substrate layer 408. Each reaction
chamber 414 may be separated from adjacent reaction chambers 414 by
chamber walls 438. In the illustrated embodiment, the chamber walls
438 have a common thickness. Optionally, interior surfaces of the
chamber walls 438 may be hydrophilic or hydrophobic. Furthermore,
an exterior surface of the chamber walls 438 that faces away from
the activity detector 420 may partially define the flow channel
410. The exterior surface may extend along a plane to facilitate
providing a desired flow of fluid through the flow channel 410
(FIG. 7). The exterior surface may also be hydrophilic or
hydrophobic.
FIG. 9 is a plan view of a single reaction chamber 414 and the
pixels 424 within the reaction chamber 414. In some embodiments,
the substrate layer 408 (FIG. 7) has a fixed position relative to
the activity detector 420 so that the reaction chambers 414 have
known spatial locations relative to at least one predetermined
pixel 424. The at least one predetermined pixel 424 detects
activity of the desired reactions from the reaction chamber 414. As
such, the reaction chambers 414 may be assigned to at least one
pixel 424. To this end, the circuitry of the activity detector 420
may include kernels that automatically associate detection signals
provided by predetermined pixels 424 with the assigned reaction
chambers 414. By way of example, when detection signals are
generated by pixels 424 shown in FIG. 9, the detection signals will
automatically be associated with the reaction chamber 414 shown in
FIG. 9. Such a configuration may facilitate processing and
analyzing the detection data. For instance, the detection signals
from one reaction chamber may automatically be located at a certain
position on an image.
Also shown in FIG. 9, in some embodiments, a detection surface of
the pixels 424 is at least partially covered or obstructed such
that the covered detection surface is unable to detect activity.
More specifically, the reaction chamber 414 has a plurality of
pixels 424, including partially covered pixels 424A and 424B and an
entirely exposed pixel 424C. The pixels 424A and 424B are partially
covered by the chamber walls 438 of the reaction chamber 414. In
some embodiments, kernels of the circuitry of the activity detector
420 may modify values of the detected activity to provide a better
representation of the detected activity within the reaction chamber
414. For example, the circuitry may include a kernel for weighting
the values of the activity detected by the pixels 424A and
424B.
FIG. 10 provides a schematic illustration of an exemplary activity
detector 432 that may be used in various embodiments described
herein. For example, the activity detector 432 may be used as the
activity detector 420 shown in FIG. 7. The activity detector 432
may be manufactured as a single chip through a CMOS-based
fabrication processes. As shown, the activity detector 432 includes
a two-dimensional array 440 of photodiodes or pixels 436 that are
communicatively coupled to circuitry 434. The array 440 is
communicatively coupled to a row decoder 442 and a column amplifier
or decoder 444. The column amplifier 444 is also communicatively
coupled to a column analog-to-digital converter (Column ADC/Mux)
446. Other circuitry may be coupled to the above components,
including a digital signal processor and memory.
FIG. 10 also includes a schematic illustration of a photodiode 436.
In some embodiments, the photodiode 436 may be configured to detect
a predetermined wavelength of light that is indicative of the
desired reactions. As shown, the photodiode 436 may include a
P-type substrate having an N-type doping region.
FIGS. 11 and 12 illustrate a fiber-optic faceplate 450 that may be
used as the substrate layer 408 (FIG. 7) in alternative
embodiments. FIG. 11 is an image showing a plan view of the
faceplate 450, and FIG. 12 is a cross-section of the faceplate 450
that is interfacing with an activity detector 452. As shown in FIG.
12, the activity detector 452 may be similar to the activity
detector 420 (FIG. 7) or, in a more particular embodiment, the
activity detector 436 (FIG. 10). The faceplate 450 may be
manufactured from a fiber-optic bundle comprising a plurality of
optical fibers of a polymer material (e.g., SU8) that are fused
together and cut to form a substrate layer or plate having a
thickness T.sub.3. The faceplate 450 may be subsequently etched or
machined to form a plurality of reaction chambers 454. The reaction
chamber 454 may have similar dimensions and functions as the
reaction chamber 414 (FIG. 7) described above. As shown, optical
fibers 458 below the reaction chamber 454 may transmit light
signals that are emitted from within the reaction chamber 454 to a
pixel 456 of the activity detector 452. In some embodiments,
circuitry of the activity detector 452 may assign at least one
pixel 456 to the reaction chamber 454 to facilitate subsequent
processing or analysis.
However, the activity detector 420 is not limited to the above
constructions or uses as described above. In alternative
embodiments, the activity detector may take other forms. For
example, the activity detector may comprise a CCD device, such as a
CCD camera, that is coupled to a flow cell or is moved to interface
with a flow cell having reaction sites therein. In other
embodiments, the activity detector may be a CMOS-fabricated sensor,
including chemically sensitive field effect transistors (chemFET),
ion-sensitive field effect transistors (ISFET), and/or metal oxide
semiconductor field effect transistors (MOSFET). Such embodiments
may include an array of field effect transistors (FET's) that may
be configured to detect a change in electrical properties within
the reaction chambers. For example, the FET's may detect at least
one of a presence and concentration change of various analytes. By
way of example, the array of FET's may monitor changes in hydrogen
ion concentration. Such activity detectors are described in greater
detail is U.S. Patent Application Publication No. 2009/0127589,
which is incorporated by reference in the entirety for the use of
understanding such FET arrays.
FIGS. 13-22 illustrate different flow covers that may be used in
various embodiments, such as in the biosensor cartridge 300 (FIG.
5) or microdevice 400 (FIG. 7). Each of the flow covers in FIGS.
13-22 include inlet and outlet ports configured to fluidicly couple
the corresponding flow cover (or flow cell) to a fluid network.
Embodiments described herein may facilitate providing a desired
flow of fluid across one or more reaction sites. For example,
embodiments described herein may facilitate providing a uniform
flow of fluid across the reaction sites. In some embodiments, flow
cells may include a flow cover that is integrally formed with a
substrate layer. In other embodiments, the flow cover may be
coupled or mounted to the substrate layer. FIGS. 13-22 illustrate
such flow covers. Furthermore, it is understood that the various
features described below with respect to the flow covers may also
be incorporated into flow cells.
FIG. 13 is a top perspective view of a flow cover 500 illustrating
a flow channel 502 in phantom, and FIG. 14 is a bottom perspective
view of the flow cover 500. The flow cover 500 may have a mounting
surface 501 (FIG. 14) that is configured to be mounted to another
element or component to form a biosensor cartridge or microdevice.
For example, the flow cover 500 may be mounted to a substrate layer
or some other base.
As shown in FIG. 13, the flow channel 502 extends between inlet and
outlet ports 504 and 506 and defines a volume in which fluid may
flow therebetween. As shown, the flow channel 502 includes an input
region 510 that receives fluid through the inlet port 504, a
diffuser region 511 that includes one or more inlet channels 516, a
field region 512 that is configured to direct the fluid across a
substrate field (not shown) that includes one or more reaction
sites, a collector region 513 that receives the fluid from the
field region 512, and an output region 514 that delivers the fluid
to the outlet port 506. Each of the channel regions 510-514 of the
flow channel 502 may be sized and shaped with respect to each other
to provide a desired flow of fluid across the substrate field.
As shown, the field region 512 of the flow channel 502 may have a
length L.sub.2 that extends along a direction of the flow of the
fluid (indicated by the arrows F), a width W.sub.2 that extends
perpendicular to the length L.sub.2, and a height H.sub.2. The
mounting surface 501 (FIG. 14) may form a perimeter of the field
region 512. In the flow cover 500, the field region 512 may be
substantially rectangular. For example, each dimension (i.e., the
length L.sub.2, width W.sub.2, and height H.sub.2) may be
substantially uniform throughout the field region 512. However, in
alternative embodiments, the field region 512 may have different
shapes and dimensions. Furthermore, each dimension may change as
said dimension extends lengthwise or widthwise.
Fluid may enter through the inlet port 504 and into the input
region 510. The diffuser region 511 receives the fluid and
separates the volume to a plurality of inlet channels 516. The
inlet channels 516 deliver the fluid to the field region 512. As
shown, the inlet channels 516 may be distributed across the width
W.sub.2 of the field region 512. The fluid flows across the
substrate field (not shown) and is removed by outlet channels 518
of the collector region 513. The fluid is then removed from the
flow cover 500 through the output region 514.
In some embodiments, the input and output regions 510 and 514
extend in a direction that is perpendicular to the field region
512. More specifically, in operation the fluid may flow through the
input and output regions 510 and 514 in a direction that is
parallel to a gravitational force direction G and perpendicular to
a flow direction of the field region 512 (i.e., a general direction
in which the fluid flows through the field region 512). Moreover,
the fluid may flow through the input and output regions 510 and 514
in a direction that is perpendicular to a flow direction through
the diffuser and collector regions 511 and 513.
The flow cover 500 may be integrally formed, for example, by an
injection molding process. More specifically, rods or columns may
extend through a void of a molding apparatus where the regions 510,
511, 513, and 514 are to be located. A block may extend into the
void as well to form the field region 512. After a resin is
injected into the void of the molding apparatus, the rods and block
may be removed thereby leaving cavities that are used to form the
channel regions 510-514. Plugging elements 520 may then be formed
or inserted into the various cavities to define the various channel
regions 510-514.
FIG. 15 is a top perspective view of a flow cover 522 illustrating
a flow channel 524 in phantom. As shown, the flow channel 524
extends between inlet and outlet ports 526 and 528 and includes a
plurality of channel regions, including a diffuser region 530, a
field region 532, and a collector region 534. The diffuser region
530 is shaped to distribute the fluid to the field region 532 and
may be oriented such that the flow direction is parallel to a
vertical axis 590. The diffuser region 530 has first and second
flow cross-sections C.sub.1 and C.sub.2 that are taken
perpendicular to the vertical axis 590. The term "flow
cross-section," as used herein, is a cross-section of a fluidic
channel that is taken substantially transverse to a direction of
the flow of fluid. For example, the flow of fluid through flow
cross-sections C.sub.1 and C.sub.2 in FIG. 15 is generally out of
(or into) the page.
As shown, the flow cross-section C.sub.1 is located closer to the
inlet port 526, and the flow cross-section C.sub.2 is located
closer to the field region 532. In the illustrated embodiment, at
least one cross-sectional dimension increases as the diffuser
region 530 extends toward the field region 532. More specifically,
a width W.sub.D of the diffuser region 530 increases as the
diffuser region 530 extends toward the field region 532. When the
diffuser region 530 reaches the field region 532, the diffuser and
field regions 530 and 532 may have substantially the same width
W.sub.D3. Also shown, the collector region 534 may be similarly
shape as the diffuser region 530.
FIGS. 16 and 17 provide a bottom view and a perspective view,
respectively, of a flow cover 540. The flow cover 540 may have
similar features as the flow cover 522. However, as shown in FIG.
16, a diffuser region 542 and a collector region 544 may have
different dimensions at respective openings 543 and 545. More
specifically, the opening 545 of the collector region 544 may have
a greater width W.sub.D2 than a width W.sub.D1 of the opening 543
of the diffuser region 542.
FIG. 18 is a top perspective view of a flow cover 550. In some
embodiments, field regions of the flow channel may be shaped to
diffuse (or expand) the flow of fluid or to compress (or contract)
the flow of fluid. For example, the flow cover 550 includes an
inlet channel 552 of an input region 554 that provides fluid to a
field region 556. Fluid may be removed from the field region 556
through an outlet channel 558 of an output region 560. As shown,
the field region 556 is oriented in a substantially horizontal
manner relative to a gravitational force direction G. The field
region 556 may be diamond-shaped such that the flow channel has an
increasing cross-section as the fluid initially flows away from the
inlet channel 552. The field region 556 may have a uniform
cross-section for a middle portion of the field region 556 as the
fluid flows therethrough, and then begin to decrease when the fluid
is proximate to the outlet channel 558. As such, the flow covers
described herein may have horizontal diffuser regions and vertical
diffuser regions as well as horizontal collector regions and
vertical collector regions.
FIG. 19 is a top perspective view of a flow cover 562. In
previously described embodiments, a flow cross-section taken
perpendicular to the flow of the fluid may have a height that
remained substantially equal to other cross-sections. However, the
flow cover 562 includes a flow channel 564 where a height in
cross-sections taken perpendicular to the flow of fluid changes. As
shown in flow cross-section C.sub.3, a height H.sub.3 of the
cross-section varies therealong. Furthermore, dimensions of the
flow cross-section C.sub.4 may also be different from the
dimensions of the flow cross-section C.sub.3. For example, the
height H.sub.4 may be greater than the height H.sub.3. Accordingly,
embodiments of flow covers and flow cells described herein may have
flow channels and, more specifically, field regions of the flow
channels with varying three-dimensional shapes to control a flow of
fluid as desired.
FIG. 20 illustrates an exemplary embodiment of a planar flow cover
570. The flow cover 570 may have a substantially rectangular or
block shape and include a height H.sub.5, a width W.sub.5, and a
length L.sub.5 that are substantially uniform. As shown, the flow
cover 570 may have inlet and outlet ports 572 and 574 that are
directly adjacent to a field region 576. As such, fluid entering
through the inlet port 572 may immediately enter the field region
576, and fluid exiting the field region 576 may immediately exit
the flow cover 570 through the outlet port 574. In the illustrated
embodiment, the field region 576 may have similar dimensions as the
field region 564. However, in alternative embodiments, the field
region 576 may have other dimensions.
FIGS. 21 and 22 are top and bottom views of a biosensor cartridge
580 having a microdevice 582 that comprises the flow cover 570
(FIG. 21) mounted to a base substrate 584 (FIG. 22). As shown, the
base substrate 584 includes an exterior side surface 586 having an
array of electrical contacts 588 thereon. The microdevice 582 may
be held by a housing 585. More specifically, the microdevice 582
may be confined within a restricted space defined by the housing
585. A cavity 589 of the housing 585 may hold the microdevice 582
such that the side surface 586 and an opposite side surface 587 do
not clear a surface of the housing 585. In such embodiments, the
biosensor cartridge 580 may be inserted into a system receptacle
(not shown) without the microdevice 582 snagging or catching a
portion of the system receptacle.
FIGS. 23-27 illustrate the system receptacle 212 in greater detail.
FIG. 23 is a perspective view of the system receptacle 212 before a
biosensor cartridge 600 is inserted into the system receptacle 212.
The biosensor cartridge 600 may have similar features as described
elsewhere, such as with respect to the biosensor cartridges 300 and
580; with respect to the microdevices 102, 235, 302, 400, and 582;
with respect to the flow cell 334; and with respect to the flow
covers 404, 500, 522, 540, 550, 562, and 570. As shown, the system
receptacle 212 is oriented with respect to a longitudinal axis 690,
a lateral axis 692, and a vertical axis 694.
As shown in FIG. 23, the system receptacle 212 includes a first
receptacle sub-assembly 602, a second receptacle sub-assembly 604,
and an actuation device 606 that is operatively coupled to the
second receptacle sub-assembly 604. The first and second receptacle
sub-assemblies 602 and 604 are vertically stacked with respect to
each other and spaced apart in an unengaged position. The system
receptacle 212 includes a cartridge slot 608 that may receive the
biosensor cartridge 600. The first and second receptacle
sub-assemblies 602 and 604 are configured to be moved toward each
other into an engaged position. In the engaged position, the
biosensor cartridge 600 may be mechanically, electrically, and
fluidicly coupled to the workstation 200 (FIG. 3). For example, in
the illustrated embodiment, the first receptacle sub-assembly 602
holds the biosensor cartridge 600 in a predetermined position. The
actuation device 606 is configured to move the second receptacle
sub-assembly 604 in a linear manner along the vertical axis into
the engaged position with the first receptacle sub-assembly 602
where the biosensor cartridge 600 may be mechanically,
electrically, and fluidicly coupled to the workstation 200.
In the illustrated embodiment, the first receptacle sub-assembly
602 holds the biosensor cartridge 600 in the predetermined position
and, as such, is hereinafter referred to as the alignment assembly
602. The second receptacle sub-assembly 604 is moved to engage the
alignment assembly 602 and, as such, is hereinafter referred to as
the mounting assembly 604. However, in alternative embodiments, the
first receptacle sub-assembly 602 may be moved toward the second
receptacle sub-assembly 604 or both the first and second receptacle
sub-assemblies 602 and 604 may be moved toward each other. Also
shown in FIG. 23, a pair of conduits 632 and 634 may be affixed to
the mounting assembly 604. The conduits 632 and 634 may be
fluidicly coupled to the fluid network of the workstation 200.
The actuation device 606 may be coupled to the mounting assembly
604 through a joint assembly 610. The joint assembly 610 is
configured to permit the mounting assembly 604 to pivot or shift
when moved toward the engaged position so that the mounting
assembly 604 may be aligned when engaging the biosensor cartridge
600. In the illustrated embodiment, the joint assembly 610 includes
a rod 612 and a pair of rotatable links 614 and 616 that are
interconnected by the rod 612. The actuation device 606 may be
coupled to the rod 612, and the rotatable links 614 and 616 may be
coupled to the mounting assembly 604. The rotatable links 614 and
616 may have inward projections 648 (FIG. 24) that engage the
mounting assembly 604. In some embodiments, the inward projections
648 may permit the mounting assembly 604 to shift along an axis
that is parallel to the lateral axis 692 and the alignment axis
695. Furthermore, in some embodiments, the inward projections 648
may permit the mounting assembly 604 to rotate along such an
axis.
The mounting assembly 604 may also include a plurality of bores 622
that extend through the mounting assembly 604 along the vertical
axis 694. The system receptacle 212 may include a plurality of
alignment pins 620 that extend through corresponding bores 622. The
alignment pins 620 are attached to the alignment assembly 602 at
one end and have a stopper 624 at an opposite end. The bores 622
may be shaped relative to the corresponding alignment pins 620 to
permit the mounting assembly 604 to pivot or shift when moved
toward the engaged position. For example, the bores 622 may have a
cross-sectional diameter that is slightly greater than a
cross-sectional diameter of the alignment pins 620.
To mount the mounting assembly 604 to the alignment assembly 602
(i.e., move the mounting assembly 604 from the unengaged position
to the engaged position), the actuation device 606 may move the
mounting assembly 604 in a linear manner toward the alignment
assembly 602. As the mounting assembly 604 approaches the alignment
assembly 602, the mounting assembly 604 may engage components or
portions of the alignment assembly 602 and/or the biosensor
cartridge 600. If the mounting assembly 604 is misaligned with the
biosensor cartridge 600 and/or the alignment assembly 602, the
mounting assembly 604 may at least one of: (a) shift along a plane
formed by the longitudinal axis 690 and the lateral axis 692 and
(b) pivot about the alignment axis 695 that extends parallel to the
lateral axis 692.
FIG. 24 is a bottom perspective view of the mounting assembly 604.
The mounting assembly 604 may include a mating face 640 that
engages the biosensor cartridge 600 (FIG. 23) and the alignment
assembly 602 (FIG. 23). As shown, the mating face 640 may include a
thermal module or element 641 and nozzles 642 and 644 of the
conduits 632 and 634 (FIG. 23). The thermal element 641 includes a
surface 650 and is configured to interface with an engagement area
of the biosensor cartridge 600 to transfer or absorb heat from the
biosensor cartridge. The nozzles 642 and 644 are configured to be
inserted into inlet and outlet ports 662 and 664 of the biosensor
cartridge 600 to fluidicly couple the workstation 200 (FIG. 3) to
the biosensor cartridge 600.
FIG. 25 is a perspective view of the alignment assembly 602. The
alignment assembly 602 may also include a mating face 652 that
engages the mounting assembly 604. The alignment assembly 602 may
include tracks or guiderails 654 and 655 that engage opposite edges
656 and 657 (FIG. 24) of a housing or casing 658 of the biosensor
cartridge 600. When the biosensor cartridge 600 is inserted into
the cartridge slot 608, the guiderails 654 and 655 may direct the
biosensor cartridge 600 to a desired slot position as shown in FIG.
25. In the slot position, the biosensor cartridge 600 may be
oriented to engage the mating face 640 (FIG. 24) of the mounting
assembly 604. More specifically, an engagement area 660 of the
biosensor cartridge 600 may face and be positioned to receive the
thermal element 641, and inlet and outlet ports 662 and 664 of the
biosensor cartridge 600 may open to and be positioned to receive
the nozzles 642 and 644.
FIGS. 26 and 27 are cross-sections of the biosensor cartridge 600
and the system receptacle 212 illustrating the mounting and
alignment assemblies 604 and 602 in unengaged and engaged
positions, respectively. In both FIGS. 26 and 27, the biosensor
cartridge 600 is in the desired slot position. As shown, the system
receptacle 212 may also include an electrical connector 666 that
electrically engages the biosensor cartridge 600 so that the
workstation 200 (FIG. 3) may communicate and/or provide power to
the biosensor cartridge 600. For example, the biosensor cartridge
600 may be able to provide detection data regarding any detected
activity of desired reactions that occurred in the biosensor
cartridge 600. In some embodiments, the electrical connector 666 is
located on a first side surface 668 of the biosensor cartridge 600
and the nozzles 642 and 644 and/or the thermal element 641 are
located on an opposite second side surface 669 (FIG. 26). The
system receptacle 212 may be configured to electrically engage the
biosensor cartridge 600 before fluidicly engaging the biosensor
cartridge 600. Alternatively, the system receptacle 212 may be
configured to fluidicly engage the biosensor cartridge 600 before
electrically engaging the biosensor cartridge 600. Moreover, the
system receptacle 212 may be configured to electrically and
fluidicly engage the biosensor cartridge 600 at substantially the
same time.
The electrical connector 666 may include a mating side 670 that
includes an array 672 of electrical contacts 674 (FIG. 26)
(hereinafter referred to as system contacts) that electrically
engage electrical contacts (not shown) (hereinafter referred to as
cartridge contacts) of the biosensor cartridge 600. In particular
embodiments, the system contacts 674 may provide a resilient spring
force toward the first side surface 668. For example, the system
contacts 674 may include pogo pin contacts or resilient beams that
flex to and from the mating side 670 in a direction along the
vertical axis 694. Furthermore, the system contacts 674 may include
a wipe surface that is sized and shaped to permit some misalignment
between one system contact 674 and the corresponding cartridge
contact.
In particular embodiments, the electrical connector 666 is moveable
to and from the biosensor cartridge 600. For example, the
electrical connector 666 may be moved in an axial direction (i.e.,
along the vertical axis 694) to and from the biosensor cartridge
600. More specifically, the electrical connector 666 may be
moveable from an unmated position as shown in FIG. 26, wherein the
system contacts 674 are spaced apart from cartridge contacts of the
biosensor cartridge 600, to a mated position as shown in FIG. 27,
wherein the system contacts 674 and the cartridge contacts are
electrically engaged. In some embodiments, the electrical connector
666 is moved through an opening or window 680 of the housing 658 to
engage the cartridge contacts.
Also shown in FIGS. 26 and 27, the conduits 632 and 634 (along with
the corresponding nozzles 642 and 644) may be separately or
independently moveable along the vertical axis 694 to facilitate
fluidicly coupling the biosensor cartridge 600 to the fluid
network. The mounting assembly 604 may include resilient springs
682 and 684 that reside within respective cavities 686 and 688. The
resilient springs 682 and 684 are configured to engage ledges of
the conduits 632 and 634 to resist movement in a direction away
from the biosensor cartridge 600. As shown in FIG. 26, in the
relaxed (i.e., unengaged position), the nozzles 642 and 644 extend
a distance D.sub.1 away from the mating face 640.
Likewise, the thermal element 641 may be separately or
independently moveable along the vertical axis 694 to facilitate
maintaining a thermal engagement with respect to the engagement
area 660 (FIG. 26) of the biosensor cartridge 600. The mounting
assembly 604 may include resilient springs 691 and 693 (FIG. 26)
that surround mounting posts that support the thermal element 641.
In the relaxed (i.e., unengaged position), the thermal element 641
extends a distance D.sub.2 away from the mating face 640. The
resilient springs 691 and 693 may resist movement of the thermal
element 641 and provide a reactive force that facilitates
maintaining the thermal interface between the engagement area 660
and the thermal element 641.
In the illustrated embodiment, after the biosensor cartridge 600 is
inserted into the cartridge slot 608 (FIG. 23) and moved to the
slot position, the electrical connector 666 may be moved to an
engaged position with respect to the first side surface 668 of the
biosensor cartridge in which the system contacts 674 electrically
engage the cartridge contacts. In such embodiments where the system
contacts 674 project from the mating side 670 and provide a
resilient spring force toward the first side surface 668, the
system contacts 674 may initially engage the cartridge contacts
before the electrical connector 666 has been fully moved into the
engaged position. If the surfaces of the biosensor cartridge 600
and the electrical connector 666 do not fully engage each other
along the interface, the system contacts 674 may facilitate
electrically engaging and maintaining the electrical connection
throughout operation of the workstation 200. Before the mating face
640 is mounted to the biosensor cartridge 600, in some embodiments,
a system controller may notify a user that the electrical connector
666 has properly engaged the biosensor cartridge 600. However, if
the electrical connector 666 has improperly engaged the biosensor
cartridge 600, the system controller may notify the user that the
electrical engagement between the electrical connector 666 and the
biosensor cartridge is improper.
As described above, the mating face 640 of the mounting assembly
604 may mount the biosensor cartridge 600 after, before, or at
substantially the same time as when the electrical connector 666
has engaged the cartridge contacts. The mating face 640 may be
moved toward the biosensor cartridge 600 by the actuation device
606 (FIG. 23). The nozzles 642 and 644 may engage the inlet and
outlet ports 662 and 664, respectively, of the biosensor cartridge
600 before the mounting assembly 604 has moved fully into the
engaged position. At this time, the nozzles 642 and 644 may be
pushed away from the second side surface 669 of the biosensor
cartridge 600 (i.e., in a direction opposite to the mounting
direction). The resilient springs 682 and 684 may resist the
movement. As shown in FIG. 27, stored (or potential) energy of the
resilient springs 682 and 684 may facilitate maintaining the
fluidic connection between the inlet and outlet ports 662 and 664
and the nozzles 642 and 644 when the mounting assembly 604 is in
the fully engaged position with respect to the biosensor cartridge
600 and the alignment assembly 602. For example, the stored energy
may maintain the fluidic connection during flow pressure changes of
an assay protocol.
Furthermore, the thermal element 641 may press against the
engagement area 660 of the biosensor cartridge when the mounting
assembly 604 is moved into the engaged position. The resilient
springs 691 and 693 may resist movement of the thermal element 641
in a direction opposite to the mounting direction (or away from the
biosensor cartridge 600). In the engaged position, stored (or
potential) energy of the resilient springs 691 and 693 may
facilitate maintaining the thermal engagement between the thermal
element and the engagement area 660 of the biosensor cartridge
600.
In some embodiments, the microdevice 628 of the biosensor cartridge
600 may be floatable within the housing 658. Dimensions of the
restricted space of the housing 658 that holds the microdevice 628
may be greater than the dimensions of the microdevice. In such
embodiments, the microdevice may slide within the housing 658 to
facilitate properly aligning the biosensor cartridge 600. For
example, if the nozzles 642 and 644 are misaligned with respect to
openings of the inlet and outlet ports 662 and 664, the microdevice
628 may slide in a lateral manner into a properly aligned
position.
Accordingly, embodiments described herein may comprise one or more
features that permit independent movement of components of the
system receptacle to facilitate fluidicly, thermally, and/or
electrically engaging biosensor cartridges. Such independent
movement may provide tolerance for mating different elements. For
example, embodiments described herein may include the joint
assembly 610 to permit the mounting assembly 604 to pivot or shift
so that the nozzles 642 and 644 and the thermal element 641 are
properly aligned with the biosensor cartridge 600. Furthermore,
embodiments described herein may include resilient springs 682 and
684 that permit the nozzles 642 and 644, respectively, to
separately move along the vertical axis 694. Similarly, embodiments
may also include resilient springs 691 and 693 that permit the
thermal element 641 to separately move along the vertical axis 694.
In addition, the electrical connector 666 may be moveable along the
vertical axis 694 and may also include resilient system contacts
674 the project a distance away from the electrical connector 666.
The system contacts 674 and/or the cartridge contacts of the
biosensor cartridge 600 may have a sufficient wipe distance to
tolerate some misalignment between corresponding contacts.
Furthermore, the microdevice 628 and/or the biosensor cartridge 600
may also be independently moveable to permit the system receptacle
212 to move the biosensor cartridge 600 when in the desired slot
position.
In alternative embodiments, other mounting mechanisms may be used.
For example, the mounting assembly 604 is not required to move in a
linear manner to engage the alignment assembly 602. The mounting
assembly 604 may be rotated about an axis to engage the alignment
assembly 602 in a manner similar to a door being moved from an open
to a closed position. In addition, the mounting assembly 604 may be
independently moveable such that a user may mount the mounting
assembly 604 onto the alignment assembly 602 after the biosensor
cartridge 600 has been placed in the predetermined orientation or
position.
Furthermore, in alternative embodiments, the thermal element may be
configured to approach and engage the biosensor cartridge 600 along
the first side surface 668. More specifically, the thermal element
and the system contacts may engage a common side of the biosensor
cartridge 600.
In addition, the resilient force generated by the resilient springs
682, 684, 691, and 693 may be generated by other mechanisms. For
example, a pneumatic system may be operatively coupled to the
thermal element 641 and nozzles 642 and 644 used to provide the
resilient force.
Although the system receptacle 212 was described above with respect
to being part of the workstation 200, the system receptacle 212 may
also be configured to operate with other bioassay systems.
Furthermore, the system receptacle 212 is not required to be
located within a workstation housing, but may be a separate
apparatus that is remotely located from the workstation.
FIGS. 28, 29, and 30 illustrate a fluid storage unit 700 that may
be used to store fluids for the workstation 200 (FIG. 3). FIGS. 28
and 29 provide a partial perspective view and a top plan view of
the storage unit 700 with a lid (not shown) of the storage unit 700
removed. As shown, the storage unit 700 includes a bag container
702, a plurality of fluid reservoir bags 704, and a waste reservoir
bag 706 (FIG. 29). In the illustrated embodiment, a fluidic control
system is configured to remove fluid (e.g., reagents, water, buffer
solution, cleaning solution, and the like) from the corresponding
reservoir bags 704 to a biosensor cartridge. After flowing through
the biosensor cartridge, the fluid may be removed and directed into
the waste reservoir bag 706. Only one waste reservoir bag 706 is
shown in FIG. 29, but additional waste reservoir bags may be
used.
As shown in FIG. 28, the storage unit 700 may include a manifold
assembly 710 comprising a plurality of tubes 712 arranged along a
side 713 of the bag container 702. The tubes 712 are configured to
be inserted into the reservoir bags 704 to fluidicly couple the
fluids of the reservoir bags 704 to the fluid network. The tubes
712 may be held by an interference fit formed by the tubes 712 and
slots 714 of the bag container 702 (e.g., the tubes 712 may be
snap-fit into the slots 714). Adjacent slots 714 may extend from a
top edge 716 of the bag container 702 at different distances so
that the tubes 712 may have a staggered relationship with respect
to each other as shown in FIG. 28. Although not shown, when the lid
is positioned over a top of the bag container 702, the lid may
facilitate holding the tubes 712 in a desired position. The tubes
712 may project from the side 713 of the bag container 702.
FIG. 30 is a side view of the exemplary reservoir bag 704 that is
formed in accordance with one embodiment. As shown, the reservoir
bag 704 may have a top end 720, a bottom end 722, and a height 724
that extends therebetween. The reservoir bag 704 may be defined by
edges 741-644. When in operation, the height 724 may extend in a
direction along the gravitational force G. In the illustrated
embodiment, the reservoir bag 704 includes a pair of opposite
flexible walls 726 and 728 that bonded together. However, in
alternative embodiments, the reservoir bag 704 may include only one
wall that includes the features described herein. The flexible
walls 726 and 728 may define a variable volume for holding a fluid.
For example, the flexible walls 726 and 728 may collapse toward
each other as fluid is removed from the volume. As shown, the
volume includes a main storage portion 730, a flow path portion
732, and a bridge portion 734. The main storage portion 730 and the
flow path portion 732 are in fluid communication with each other
through the bridge portion 734. Furthermore, the reservoir bag 704
may include a bag opening 736 that is located proximate to the top
end 720. The bag opening 736 is configured to fluidicly engage a
corresponding one of the tubes 712.
As shown in FIG. 30, the reservoir bag 704 includes a partition 740
where the flexible walls 726 and 728 are bonded together that
extends from the top end 720 (or top edge 741) and toward the
bottom end 722 (or bottom edge 743). The partition 740 may extend
to a distal tip 745 that is proximate to the bottom end 722. As
shown, the bridge portion 734 is located between the distal tip 745
and the bottom end 722. In the illustrated embodiment, the main
storage portion 730 of the volume is greater than the flow path
portion 732 of the volume. Furthermore, the bag opening 736 may be
located at distance D.sub.2 away from the top end 720 or top edge
741. The distance D.sub.2 may be configured to permit some air to
collect proximate to the top end 720 in the flow path portion 732
without the air being removed through the bag opening 736.
Accordingly, when the fluid is removed from the reservoir bag 704,
the fluid flowing from the main storage portion 730 flows to the
flow path portion 732 through the bridge portion 734. Fluid from
the flow path portion 732 flows through the bag opening 736 to the
fluid network. As such, fluid is drawn from proximate to the bottom
end 722 to reduce a probability of air being removed with the
fluid. As shown, air may collect within the volume proximate to the
top end 720 in both the main storage and flow path portions 730 and
732.
In the illustrated embodiment, the flexible walls 726 and 728 are
bonded by heat-pressing portions of the flexible walls 726 and 728
together. In particular embodiments, the flexible walls 726 and 728
may be heat-pressed in a single heat-pressing step to form the
partition 740, the edges 741-644, and the bag opening 736 of the
reservoir bag 704. However, in alternative embodiments, the
flexible walls 726 and 728 may be held together by alternative
methods, such as an adhesive or a suitable thread.
It is to be understood that the above description is intended to be
illustrative, and not restrictive. For example, the above-described
embodiments (and/or aspects thereof) may be used in combination
with each other. In addition, many modifications may be made to
adapt a particular situation or material to the teachings of the
invention without departing from its scope. While the specific
components and processes described herein are intended to define
the parameters of the various embodiments of the invention, they
are by no means limiting and are exemplary embodiments. Many other
embodiments will be apparent to those of skill in the art upon
reviewing the above description. The scope of the invention should,
therefore, be determined with reference to the appended claims,
along with the full scope of equivalents to which such claims are
entitled. In the appended claims, the terms "including" and "in
which" are used as the plain-English equivalents of the respective
terms "comprising" and "wherein." Moreover, in the following
claims, the terms "first," "second," and "third," etc. are used
merely as labels, and are not intended to impose numerical
requirements on their objects. Further, the limitations of the
following claims are not written in means-plus-function format and
are not intended to be interpreted based on 35 U.S.C. .sctn.112,
sixth paragraph, unless and until such claim limitations expressly
use the phrase "means for" followed by a statement of function void
of further structure.
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